So I had this idea the other day while listening to the FTL soundtrack. What about an X-Com game where the UFO intercept part is basically the FTL combat system (with gunships large enough for multiple crewmembers who can walk around in their ships)?
I think the two systems would synergize really well. Take enemy systems --on the one hand, you can weaken UFOs by destroying their systems (weapons, shield gens, etc.), but on the other hand, any system you destroy you won't be able to salvage after you've recovered the crashed UFO.
Also, it'd add a reason to engage the UFO up closer if only some weapons could target specific rooms/systems. Using UFO Defense as an example, Avalanche missiles could be safe standoff weapons, but short-range missiles and guns would allow you to target out aliens or specific systems.
Also, the same way your ship in FTL gets more and more damaged over time, your gunships in this X-Com game could repair very slowly, so that they'd get more and more damaged with subsequent UFO dogfights. You'd have to prioritize what to repair (hit points or various systems), and you'd have to make decisions as to when to intercept and when you have to let your gunships wait and repair.
You could also play around with FTL-like gameplay systems by having the player unlock scanners that allow you to look inside UFOs so you know what to target, better engines for higher evasion percentage, etc. Maybe instead of unlocking just unlocking new ships, you research and unlock new components and whatnot for your gunships.
Also, since anyone on the ship can get injured during a fight, you could give players the option of putting soldiers on the same ships that shot down UFOs, you could risk putting soldiers on the same ship you use to shoot down UFOs, knowing any of them might get killed during an aerial dogfight.
So is there any X-Com game that has played around with this particular system? If not, feel free to toy around with the idea --I'm busy with my current game and I doubt I have the experience and skill to make a full-fledged X-Com game anytime soon anyway :P .