Some things I've always wanted in an FPS:
1: A gun that shoots knives
2: A gun that shoots proximity mines
3: A gun that shoots other guns, so your friends can pick them up and shoot people with them
4: Your choice of either personal shields that protect against melee, personal shields that protect against ranged attacks, or a motion sensor that gives you a local map with IFF. Expand this into other equipment ideas. Point is you can't have it all. But if a player is being a punk and knifing everyone for fun, they can spawn with melee shields and stop his ganking.
5: Barbed wire gun is an excellent idea. The first piton shot trails a line of barbed wire to your gun. If you move, you sweep the barbed wire along. The next shot fires another piton which anchors the line between the two, but your gun is connected to Piton 2. You automatically reel in or pay out slack as you move closer or farther. If you run out of wire it just lands on the ground there and can be blown around by explosions, wind, water, etc. Better is to fire a last piton and anchor the end, then either move out of wire range or else alt-fire to cut the wire.
Your gun has a supply of pitons and a supply of wire. You can reload the pitons anytime from an ammo source but to reload the wire you have to eject the current spool and load a new one.
This idea could be used for playing out wire for engineering projects and for ropes for climbing.
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It would be nice if you made equipment work so the player built his own things. For example, instead of a proximity mine as a single item, include a motion sensor, wires, a detonator, and an explosive. Then if you just add a radio transmitter and a radio receiver you automatically have a radio detonated bomb. Add a digital timer and you get a time bomb. Add a heat sensor and a fire-extinguisher-explosive and he can make a fire control system. You see?
I hear this is kind of like how Space Station 13 works.
This way engineers and demolitionists actually feel like they're doing the thing they're playing, like how a spy feels like a spy because he infiltrates and sneaks, or a marine feels like a soldier because he runs around shooting things.
The medic should have pretty good healing abilities that come out of a kit, which needs replenishing at a medical storehouse or cabinet or sickbay. Perhaps he should need to perform certain tasks for certain wounds - for example, he actually needs to inject painkillers if the patient seems to be in pain (or asks for them), he needs to scan the person to detect wounds (or just hope he can see everything), disinfect, use tools to remove shrapnel or infected tissue, bandages, splints, give antibiotics, more painkillers, probably an adrenaline shot to get him back on his feet, salve for burns, neutralizers for chemical burns, all depending on what the injuries were. This way he feels like he's actually a medic.
Certain places should make you more effective just because there are better stationary tools around. A medic should be able to work faster and better in a hospital. The engineer should be able to do a lot of crazy stuff from main engineering. A security station should have panels for opening/closing/locking/unlocking doors and hatches and valves, releasing stun gas, setting off or canceling alarms, viewing through security cameras, turning remote turrets on or off.
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You definitely need vehicles. Go for vehicles that have specific game effects. Example:
Skirmisher-type fast vehicle like a jeep with a machine gun pintle mount
Tank-type mobile anti-vehicular vehicle
Artillery-type anti-everything vehicle (but with less armor and slower aiming)
Personnel carrier-type armored but with no weapons or just a single machine gun thing
The vehicles should each have a few loadout variants. Examples:
Skirmisher: MG (standard), Partisan (explosive packs vs buildings), Comm (acts as comm beacon for expanding zone of command or just radio communication and sensors)
Tank: Big Gun (standard), Flamethrower
Artillery: Big Gun (Standard), Rockets
APC: Personnel (Standard), Ammo (carries a whole lot of ammo for vehicles and people), Medical (carries a lot of medical supplies and a couple pieces of large medical equipment), Engineering (more tools and repair supplies)
This should extend to planes (shuttles, dropships, bombers, whatever) and submersibles (possibly amphibious) and hovercraft.
It would be awesome if you included other vehicles that are less than optimal in a fight. Trucks, regular commuter cars, and especially motorcycles.
In fact, if you add just one vehicle, it must be a motorcycle.
If you could figure out how to do modular vehicles, where you assemble a design and then build it, that would be amazing. Modular spaceships? Play a grease-monkey who is saving up for the best engine parts for his sweet vintage motorcycle?
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You need a built-in voice chat. Only people who are on your comm channel, with the channel password, and who are in range of a comm beacon, can chat in your channel. So when you log in your team picks a channel and a password, and then you want to get out there and plant comm beacons around so your friends are always in comm range.
If you talk and you aren't holding the comm button, the speech is sent to the other nearby players as if you had said it from your position. So you can give yourself away if you make noise in person.
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Add physical emotes like pointing and waves so people can communicate silently if they want.
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Consider adding basically everything from Wolfenstien: Enemy Territory. Things like smoke and poison gas grenades, binoculars used to spot mines for your friends, weapons include flamethrower, mortar, bazooka, man-portable (but needs to be entrenched) machine gun, different types of explosive for mines, grenade launchers (not the same as a rocket launcher or missile launcher), spies that can steal uniforms, field ops being able to call in airstrikes or artillery, ability to kick a thrown grenade or airstrike flare or gas canister.
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Different weights of personal armor like in Tribes 2. Heavy armor is more protective. Also base stations that can be built to help the team and stationary turrets (those are also in Team Fortress?)
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Definitely needs to be objective-based. People need to always have something to do, whether defending or attacking, and unless the other side is just sitting around a defender will always be able to reinforce the defense somehow.
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Different ammo types. One is good against armor, but punches through (possibly hurting someone behind). Another fragments when it hits, which is bad when it hits armor but will deliver all its damage to the target instead of punching through. It also reduces collateral damage like poking a hole in a wall panel leading to a power conduit or fuel line or into space. You should have non-human mobiles for each type also, so robots are hurt more by the AP rounds while animals and aliens and such are hurt more by the EX rounds.