Yes, FTL! Definitely FTL, at least as an option! (Pay no attention to MOO3 this time, the fact that it combined warp points with FTL is NOT the reason that it sucked

)
Also, this is a bit cheesy, but how about shields and even armor that only works some of the time, or only covers specific components? You know how in Star Trek if they get the shield frequencies right they can get right through the shields? Well, something like that, only on the order of seconds instead of milliseconds. (And remember the Metools from Megaman? They were invincible... except for a second or so after they opened their shells to shoot! Wouldn't it be fun to install an impenetrable armor plate on your weapons, but require it to be opened in order to actually shoot? Gives you the real "evil overlord" effect

)