Touhou and Assassin's Creed.
I've already seen a few doujins about this concept/crossover.
Anyway, I've thought of a few special abilities for several of the characters already (send help)...
Lore/story for each of the characters would have to be different for every character. Which would probably take the writers years if they even bothered.
All characters:
+ Longer Jumps
- No Eagle Vision
- Guards become more suspicious more easily in certain eras (because there were times where women didn't typically carry weapons)
Reimu Hakurei:
+ Guarding in combat creates a barrier that can stun enemies for one or two seconds, allowing the player to do literally whatever they'd like - kill, evade, etc.
+ Character-specific weapons: Reimu's Gohei and Reimu's Amulets. The Amulets act like smoke bombs, but with the targeting and range of throwing knives (up to three people at once, that is). The Gohei is a fairly weak melee weapon that makes the barrier more effective.
Marisa Kirisame:
+ Character-specific weapons: Marisa's Mini-Hakkero and Marisa's Broom. The Broom can be used to fly and as a fairly weak weapon in combat, the Mini-Hakkero shoots a smaller version of the Master Spark, that only hits one person at a time. It deals enough damage to kill most enemies in a single hit.
+ When pickpocketing, people take longer to notice they've been robbed.
+ Finds more money than other characters.
+ Auto-loot upon assassination.
+ Faster loot speed.
Reisen Udongein Inaba:
+ All guns aim and reload faster. Finds bullets more frequently.
+ Can target enemies with her eyes to, after a few seconds, induce the effects of poison (except targets bodies are rolling around as if they were defeated with the fists in the end). Some of her melee finishers can have this effect as well.
+ Medicine and Poison are more effective.
Youmu Konpaku:
+ Sword stats are boosted.
+ Character-specific weapons: Roukanken (lit. "high-building sword") and Hakuroken (lit. "plain-building sword"). Take up the sword/medium weapon slot, capable of finishing two enemies at once (similar to the twin Hidden Blade's Double Assassination).
+ Finisher animations take moves from Kendo and other katana-related martial arts.
- Difficult to hide among crowds due to her ghost half.
Rumia:
+ Can perform an ability similar to the smoke bomb.
Cirno:
+ Can summon patches of ice to slip enemies.
+ Can fly short distances.
+ Taunts are more effective.
- Difficult to hide among crowds due to her wings.
Hong Meiling:
+ Boosted stats with all weapons, especially the fists.
+ Capable of chaining "kills" with the fists.
+ Finisher animations draw moves from various Chinese martial arts.
Patchouli Knowledge:
+ Capable of using spells to kill or confound enemies.
+ Can fly short distances.
- Low health, cannot sprint or parkour without occasionally having violent coughing fits. These coughing fits also make hiding (both in hiding spots and in general) difficult.
Sakuya Izayoi:
+ Boosted stats with knives/small weapons, as well as with throwing knives.
+ Capable of stopping time for a few seconds.
Remilia Scarlet:
+ Runs and attacks faster.
+ Attacks can break an opponent's guard more easily, and deal more damage. Can disarm and counter opponents who normally can't be disarmed or countered.
+ Can transform into a bat and fly.
+ Can fly short distances.
+ Finishers with fists have a blood drinking animation, which restores a bit of health. Still doesn't kill.
- Drinking blood increases your notoriety a LOT (for games that have that mechanic.) Witnesses also react very poorly. Town criers/heralds will call her a "bloodthirsty monster" and similar remarks when notoriety is high enough.
- Difficult to hide among crowds due to her wings.
- During the day, Remilia cannot be used. If she's the current active character, she automatically returns to the headquarters/bureau/safehouse, where another character must be selected.
Flandre Scarlet:
+ Can kill almost any enemy in a single hit, even if they block.
+ Moves quickly.
+ Can fly short distances.
+ Can clone herself, similar to the ability to summon Assassins.
- Difficult to hide among crowds due to her wings.
- Cannot be used until a certain point in the story.
- During the day, Flandre cannot be used. If she's the current active character, she automatically returns to the headquarters/bureau/safehouse, where another character must be selected.
Alice Margatroid:
+ Can use dolls to attack or retrieve items from a distance. These dolls can also search and pick up dead bodies.
Yuyuko Saigyouji:
+ Can assassinate any enemy when they are targeted.
- This power is restricted to assassination targets
+ Can fly short distances.
+ When dodging, she does not actually move, instead becoming incorporeal for a moment. This allows her to follow up by attacking.
Aya Shameimaru:
+ Moves and attacks very fast.
+ Can fly short distances.
Keine Kamishirasawa:
+ Headbutts deal much more damage than other attacks.
+ Several/most of her melee finishers end with her headbutting the target.
+ Can conceal history to exclude her existence, enabling her to become anonymous in almost a few seconds once line of sight is broken.
+ Turns into a were-hakutaku on some nights, allowing her to deal much more damage, especially with headbutts.
+ The were-hakutaku form has a seperate notoriety meter, meaning that Keine's human identity won't be compromised.
- The were-hakutaku form gains notoriety much faster and cannot hide in crowds. The town criers/heralds will refer to her were-hakutaku form as a "merciless beast" or similar when notoriety is high enough.
Erin Yagokoro:
+ Can refill her own medicines and poisons for a higher price than at stores, as well as those of the other characters (when playing as the other characters, talk to Erin in the hideout/safehouse/bureau.). These medicines and poisons are much more effective than the ones purchased at stores.
+ Bows and crossbows aim and reload faster.
+ No health bar, as she's immortal.
Kaguya Houraisan:
+ No health bar, as she's immortal.
+ Manipulating eternity to speed up time, but cannot slow it down past normal speed of 1 second per second.
+ Character-specific weapons/equipment: Seven Treasures. These treasures take the place of an Assassin's standard gear, allowing Kaguya to cast powerful magics.
- Using the treasures to cast magic in direct combat causes notoriety to increase much more quickly. Town criers/heralds will call her out on her "destructive and forbidden magics" when notoriety is high enough.
Fujiwara No Mokou:
+ No health bar, as she's immortal.
+ Can manipulate fire to burn enemies. Acts similarly to the crossbow but with effects surprisingly similar to poison, but much faster to kill (enemies flail about wildy before dropping dead).
+ When destroying buildings (like the Borgia towers in Brotherhood), her animation involves tossing a fireball instead of a torch.
- Use of fire will cause Mokou to gain notoriety faster than normal. Also, the town criers/heralds will call her a "pyromaniac" and similar remarks when notoriety is high enough.
Yuuka Kazami:
+ Character-specific weapon: Yuuka's Parasol. This parasol can be used to block all kinds of attack, even bullets. It can also shoot smaller versions of the Master Spark, similar to Marisa's Mini-Hakkero.
+ Attacks in melee deal more damage and break guards more easily.
+ Can intimidate people (effect of bribing heralds for free, discounted shop prices).
Komachi Onozuka:
+ Character-specific weapon: Komachi's Scythe. A very effective weapon that can also be used to intimidate people, similar to Yuuka's ability.
+ Can manipulate distance to perform a teleport of sorts.
- Using/carrying the scythe makes it impossible to hide in crowds, due to the scythe's imposing appearance.
Eiki Shiki:
+ Can determine if a person is good or evil, like a monochrome version of Eagle Vision.
+ Character-specific weapon: Rod of Remorse. Deals much more damage versus evil targets.
+ Character-specific item: Cleansed Crystal Mirror. Drastically changes the post-assassination cutscenes. Can also be used against evil enemies to create a clone that attacks them.
- Instantly desynchronizes upon killing an innocent/causing an innocent's death.
- Cannot perform actions like bribery or pickpocketing.
Nitori Kawashiro:
+- Not a playable character, instead taking the role of Leonardo Da Vinci.
Momiji Inubashiri:
+ Moves quickly.
+ Attacks deal more damage and break guards more easily.
+ Character-specific weapon: Momiji's Sword and Shield. A very effective medium/sword weapon that replaces the kick with a shield bash, dealing more damage and causing more knockback.
Sanae Kochiya:
+ Can cause small miracles to aid her - A pursuer trips, causing the ones behind the pursuer to stumble, a pursuer's horse gets a cramp, an enemy's weapon jams or breaks, etc.
Byakuren Hijiri:
+ Boosted stats with all weapons (but see below).
+ Moves quickly.
+ None of her finishers kills the opponent.
+ Gains less notoriety.
+ Performs knockouts instead of assassinations. Can thus perform a hiding spot/cover knockout, a aerial knockout, and a double knockout.
+ Apprehends targets instead of killing them, drastically changing the story.
+ Can mingle with crowds much more easily.
+- Taunts encourage enemies to surrender rather than goading them into attacking.
+ Civillians/ordinary citizens will sometimes help her in a similar manner to the vigilantes in Brotherhood, grabbing a guard by the arm and not letting go.
- Immediately desynchronizes upon killing anyone. Cannot perform assassinations of any kind.
- Cannot use the gun, the hidden blade, poison, the crossbow, throwing knives, and in fact most other lethal weapons.
- Cannot perform ledge/hanging knockouts, as those would cause the target to fall and die.
- Cannot perform certain actions like bribery or pickpocketing.
Parsee Mizuhashi:
+ Can create a copy of herself similar to a Summon Assassin ability.
Yuugi Hoshiguma:
+ Attacks deal much more damage and break guards much more easily.
+ Headbutts are lethal.
+ Can knock out enemies in just three steps.
+ The taunt button can be held down to perform a shout that scares enemies, deals damage, and knocks enemies back a significant distance.
+ When buildings need to be destroyed (like the Borgia towers in Brotherhood), Yuugi simply punches and kicks them.
Satori Komeiji:
+ Can tell whether or not she's being watched, especially by guards.
+ Can read minds. This can change cutscenes quite dramatically.
+ Can copy the attacks, moves, and demeanor of allies and enemies to some extent.
- Doesn't do well in crowds.
Koishi Komeiji:
+ Cannot be detected unless directly in someone's line of sight. If she moves out of sight when someone's looking at her, they'll forget she even exists.
+ Immediately becomes anonymous when line of sight is broken.
+ Gains very little to no notoriety.
Nazrin:
+ Can find items, loot, and money much more easily than other characters.
+ Auto-loot upon assassination.
+ Faster looting speed.
+ Automatically knows the location of treasure chests and other collectibles on the minimap when synchronizing with viewpoints.
Kogasa Tatara:
+ When exiting hiding spots, can surprise guards and passerby to restore a bit of health and provide a brief stun of one or two seconds.
Ichirin Kumoi:
+ Character-specific weapon: Ichirin's Rings. Replacing the fists, these rings allow her to use her powerful companion Unzan to punch enemies. This doesn't require a finisher animation to defeat them.
Minamitsu Murasa:
+ Can fly sort distances.
+ Can assassinate targets who are near water by causing them to fall in the water and drown. She can even capsize ships if she wishes.
+ Character-specific weapon: Minamitsu's Anchor. A heavy weapon that can be thrown to hit enemies at range.
- Cannot swim and will immediately exit the water if she falls in. (Since she drowned, she probably has bad memories with water and swimming)
Shou Toramaru:
+ Character-specific weapon: Shou's Spear. A good weapon with a long reach.
Nue Houjuu:
+ Can disguise as a nearby passerby, or even as a guard, without using any items. Only works as a form of hiding once line of sight is broken.
+ Can disguise rocks as coins, making the money toss ability free for her.
+ Can fly short distances. Hides her wings when not using them, allowing her to blend in with crowds.
Iku Nagae:
+ Can sense the general attitude towards her, and whether people will help, run away, or call the guard if she gets in a fight.
+ Character-specific weapon: Iku's Scarf/Shawl. Replaces the fists, and disarms more easily.
+ Can create lighting to shock enemies.
Tenshi Hinanawi:
+ Character-specific weapon: Sword of Hisou. A very powerful sword.
+ Can manipulate the earth to boost herself up onto a ledge, or to trip an enemy.
Kyouko Kasodani:
+ Can manipulate sound to deafen an enemy's ears and affect their balance, effectively creating a guard break.
Yoshika Miyako:
+ Can take much more damage than other characters.
+ Bites people when using finishers, turning them into Jiang Shi as well. These fight for her side.
- Limited to fists/bare hands as weapons.
- Cannot free run, assassinate, perform leaps of faith, or pickpocket.
- Biting majorly increases notoriety.
- Her inflexibility and constant outstretched arms make it impossible for her to hide in a crowd.
Seiga Kaku:
+ Can pass through walls and into buildings, increasing loading times as the Animus must now load interiors as well as exteriors.
Soga no Tojiko:
+ Can fly short distances.
+ Can create thunder to spook or distract opponents.
Mononobe no Futo:
+ Has an additional throwing weapon, plates. These are nonlethal weapons that hit their targets fairly easily, due to their large size. Several plates can be summoned up by Futo and then launched at enemies.
Toyosatomimi no Miko:
+ Can listen to people's desires, which can drastically change cutscenes. She can also thus sense whether guards have noticed her or not, and thus whether performing certain actions will attract the notice of guards.
+ Character-specific weapon: Shichi-sei ken (Seven Star Sword). An excellent sword that can shoot bolts of energy.
+ Character-specific weapon: Miko's Shaku. A small ritual baton that makes for an okay small weapon.
Mamizou Futatsuiwa:
+ Can disguise herself as a passerby or even as a guard without using any items. She can also disguise rocks as coins, making the money throw ability free for her.
+ Can turn opponents into harmless animals, or turn their weapons into something useless.
Hata no Kokoro:
+ Can manipulate emotions to scare people, particularly enemies, causing them to run away or surrender.
Utsuho Reiuji:
+ Can fly short distances.
+ Character-specific weapon: Yatagarasu Cannon. An extremely powerful arm cannon that can also be used as an effective bludgeon.
- Equipping the cannon takes quite some time, and thus can only be done while in a hideout.
- Equipping the cannon disables free-running.
- Equipping the cannon disables the use of most weapons, like daggers, swords, etc.
- Equipping the cannon makes it difficult to hide in crowds and benches, due to its unusual appearance.
- Shooting the cannon increases notoriety at a much faster pace, and risks hitting innocents who are nearby.
Sekibanki:
+ Can detach her head to scout ahead (pun not intended) without exposing oneself as easily.
+ Can detach her head when hit to fake death.
+ Can multiply and detach heads, and then use them as throwing weapons.
Kagerou Imaizumi:
+ Turns into a were-wolf on some nights, increasing physical stats.
+ The were-wolf has a separate notoriety meter, meaning Kagerou's human identity won't be compromised.
- The were-wolf gains notoriety much more easily. The town criers/heralds will refer to her were-wolf form as a "merciless beast" or similar when notoriety is high enough.
- Difficult to hide in crowds due to her tail.
Seija Kijin:
+ Can flip enemies and targets over at will.
+ Very good at countering attacks.
- Attracts attention more easily, due to her demeanor/nature.
Shinmyoumaru Sukuna:
+ Character-specific weapon: Shining Needle Sword. An excellent sword that appears to be an oversized sewing needle.
+ Character-specific weapon: Miracle Mallet. An inchling artifact that is too dangerous to use for anything but fairly small wishes, like the wish to become larger or smaller. Sukuna can use this item to shrink and hide much more easily.
Raiko Horikawa:
+ Can make all her enemies follow a predictable attack pattern in combat.
Sumireko Usami:
+ Can teleport short distances.
+ Can fly short distances.
+ Can disarm or knock over enemies with psychic power.
+ Can throw fireballs.
+ Can use astral projection to view areas without being physically present.
Clownpiece:
+ Can drive people insane, with effects similar to fast-acting poison (flailing about wildly before collapsing).
Hecatia Lapislazuli:
+ Can split into three bodies, which aid in combat similar to Assassin recruits.
I got pretty much everyone (from the games, at least) I could think of with a useful ability/one that I could put into gameplay.