Hey, I'm just daydreaming. This would be the “everything you could ever want from a FPS” FPS game, and it would be based on the Jihad. You might need a dual Alpha to run it, but it'd be really cool. [EDIT: Boy, does that date this concept.]
Yes, we've got sword fights and hand to hand combat alongside the gunfights, mountable vehicles ranging from motorcycle to mech to jetfighter, characters ducking, diving, jumping, rolling, pulling, pushing, and crawling, objects that can be usefully used, thrown, dropped, and swung, unique magical skills, shapeshifting for those shapeshifting Jihaddi, and all of this with a keyboard and mouse interface that's simpler and easier to use than Doom's was!
Current status: a joke.
Development difficulty: impossible.
There's a game map with a bunch of levels, you can go from certain levels to others (the levels are literally cities on the map). Jihaddi are stationed in certain cities, you pick one and fight your way out of it, then go wandering around blowing up stuff in other cities.
The story mode involves huge alien anenome-like lifeforms triple the size of a wal-mart planted on the land and looking ugly and evil while spraying passing anything with sharp bits of itself. They can down helicopters from a few miles out, and eventually the Jihad has to clear 'em out somehow. Don't ask what deep reaches on my mind these came out of, I don't know. (Looking back, it was probably Crono Trigger)
If a Jihaddi is injured enough that you don't want to risk them fighting any more, you can find a safe area, exit the level, bring another Jihaddi in with first aid kits in their inventory, fight their way to the injured Jihaddi and heal them. If the baddies reach the injured Jihaddi first, the AI fights for the injured.
My concept involved the deathmatch map being the entire city of San Francisco rendered in the game engine, plus the bay for naval battles. Hey, I said it was a daydream.
There can also be starfighters that could be launched into outer space to battle Lyran ships there. And we can have a secret level where original Wing Commander ships are rendered in this game engine that allows for outer space battles, since it's not utter munchkin enough already. And you can wander around on and board these ships since it's an FPS at core, shooting up Kilrathi and making the bonus secret level better than the full actual WC games were.
Jihaddi have different skills (run/walk speed, jumping, aiming, arm strength, carry strength, hit points, etc) and can level up by shooting enough baddies. Aiming as a skill is important because the computer will automatically fudge your aim! It will do this for the enemy too, randomly putting the shot somewhere in a cone in the general direction of where you or the AI wanted. When you get off a shot, the recoil means your weapon no longer aims in the same direction either, so you end up just spraying an area or needing to re-aim.
Since playing Thief, I decided that stealth and conking people over the head is as important as shooting them, so this is implemented as well! Don't ask how. My idea is that hits to the head lead toward unconciousness, and a character who is at rest (by being away from battle from a while and from not running and other factors) is very susceptible to being KO'd in one shot.
The Lyrans show up, as do sponge minions (dumb bad guys), wyrm minions (smarter bad guys), and their interstellar slave fauna.
As in JRTS, there are police and military guys as well as civilians. The military tend to kick ass wherever they get involved, but are few in number. You can interact with NPCs enough that the police can order you to drop your weapon, or aggressive military forces may become friendly to you if you help them fight off baddies.
And yes, it's time for another “as if the game wasn't munchkin enough already”: Let's have the Doom monsters show up as out-of-control allies of the demon-summoning Lyrans, and Duke Nukem shows up as an unnamed war hero who you have to protect from an assassination attempt in one mission.