I had this idea for a Alpha Protocol/KOTOR-esque Warhammer 40k RPG based around being an Inquisitor, some points I thought up:
Combat would be a XCOM style turnbased with a party (your an inquistor with perhaps a techpriest for buffing/tech support, maybe a stormtrooper who can use heavy non-powered armor and heavy weapons, etc.)
You can bring in two sets of weapons, and change them freely each round, either 2 full size weapons (las-rifles, bolters, etc.) or 1 melee weapon and 1 ranged weapon (you have a choice to take cover and use a regular snap shot with the pistol, or if the enemy's close enough, you can run up and engage in melee)
Melee acts like a normal combat round of D&D, with some warhammer thrown in, ya know, a attack round and a defense round, and if the enemy rolls a 20 or similar, they get a melee counter hit in. Or rarely, if you roll a 20 and they roll a 20, you get this awesome "duel" animation, and the game rerolls to settle it.
Ranged of course, is standard XCOM, maybe with KOTOR-style mechanics with some feats letting you choose to do a full auto burst (five attack rounds at reduced accuracy, for instance) or a sniper shot for critical damage.
As for character creation, you can choose the Ordo you belong to:
Ordo Xenos Inquisitors would be the "guile" heroes, relying on stealth, diplomacy, and good guns to get by
Ordo Malleus Inquisitors are the "warrior" types: loud, heavy powered armor and the best melee weapons (imagine whacking a chaos marine in the face with a thunder hammer, for instance
Ordo Hereticus Inquisitors are the "mages", powerful psyker abilities and the ability to root out info directly from targets minds
There would be a feat/power tree for each Ordo, for example, Ordo Xenos get access to extended diplomacy feats, allowing deeper conversations with any affable xenos you come across for info or temporary alliances (with impact on the story!), while Malleus guys can add an extra attack round to melee engagements that uses their small ranged weapon after a melee combat round, giving them a free shot after a melee round. Hereticus guys get to blast things with fire and call in powerful psyker support.
Speaking of info above, you're going to have to dig some info up, Alpha Protocol-style throughout the game, the Inquisitorial Libraries might be full of good info but some secrets have to be found out first hand and must be crosschecked with what you know, as some questgivers will out-right lie to you cuz they might be in on something heretical or incriminating. And just like Alpha Protocol, what you know and what you do and how you do it affects the story. Being a "PURGE THE HERETICS!" type will make sure all of the local factions know you're there and you mean business, opening up info through intimidated parties. However, you can go incognito, like Amberly Vail, and collect what info you can before revealing yourself (not like that).
You are assigned to one of 3 overarching stories in a certain sector of space based on your chosen Ordo. 3 separate enemy plots are coming together, and while you might be working to stop one, you'll get some crossover into the other plots, affecting your story. Standard Obsidian style plot; 3-5 planets with individual stories that need solving, but each one ties into the over arching story for your Ordo, and there's some crossover based on your story so far and what you did/how you've been playing.
I literally came up with all of this while reading the Ciaphas Cain novels and drinking coffee while waiting for my plane home a few days ago.