As I think, KSP reached point when community do more to the game than official updates. Game still is not optimized as well, and a lot of things community made should be in the stock game.
Optimization is the thing we all want.
KIS and KAS in stock game.
Life Support that we can disable if we want.
Real Solar System (If you are creating new save it should be an option to use Kerbal system or RSS).
OPM and other planet mods, so you can enable or disable planets from these mods in stock.
Manned planet exploration is a bit boring, but what about caves? What about geysers so you can get electricity on your base?
Included USI, Near Future, Color Coded Canisters, Community Tech Tree, Unmanned Before Manned, Engine Lighting, Planet Shine and also more Graphic mods.
Graphics in the stock are bad. Very bad. What about simple atmosphere and water? Simple version of Scatterer will be enough, but stock clouds will be even better.
Kerbin not to look like lifeless planet with only our buildings.
Parts with reflection (Also graphics, but that will look good).
"Portrait stats" in the stock.
"TakeCommand" to launch kerbals in the seats.
"Trajectories" in stock. If something in carrier is upgraded, maybe add an option to predict landing place and aerobraking at atmosphere?
Transfer Window Planner.
"Precise Maneuver" mod?
"Time Control" mod with all it's features.
A bit more antennas for really far travelling.
SSPXr and colonization. You can make it into DLC, still with life support will be awesome.
Aerodynamics, of course based on real ones.