I might as well start off, as i have a few things I'd love added.
1.) Every time you beat the flagship, a random flagsip weapon is unlocked. They would act like the arty beam in which they are their own system, with 3 upgrades. (like the flagship). You could only have one on at a time, but advantiges would be they wouldn't be dependent on the weapon system.
2.) A mode where every time you die in the game, (or beat it) the amount of scrap collected goes to the hangar, which once defeating the final boss unlocks a new mode: Federation mode, as you use the scrap you have to build new ships for your fleet, based on ones you have unlocked. (and as you play ftl, you could get ships to join). You would take part in sending fleets of ships destorying rebal camps, and choosing how much scrap to give to a ship for upgrades and new weapons.
3.) More drones. 'nuff said.
4.) Sort of a cheat mode in-game. One that lets you repair yourself, give you as much scrap as you want, any weapons, ect, but nothing there would count to acheves. It would be cool to test out stratigys.
5.) more events. we have a nice amount of 'em right now, but more would always be wonderful

So, what do YOU want in FTL?