Wow, really good thread this and some fine ideas.
Personally i would hope for keeping current subfactions, or at least some of them (i could see one faction comprised of TL, AR and VR with completely new ships and techs, then i would like keep TR, AL and especially VL as basically advanced versions of vanilla sins factions and then perhaps one new faction (but not what chases the Vasari).
I would like to see technical improvement of the engine (multicore, 64 bit, way better graphics), but artistic wise i would like to keep some of the current ship and structures (like my favs Kortul, Vulkoras, Orkulus, Vorastra, Ruiner, Kol, Marza, Argonev, Discord, etc...) just with more polygons and details on them... just because i consider these ships to be brilliant and therefore pointless to replace with something new and potentially less appealing.
Gameplay-wise, i want to see bit more life in the game, things like minor races or unique planets, all of that with their own special properties, abilities, ships and stuff....i mean, what bugs me most is, when you capture/bomb enemy homeworld, how it feels exactly the same like any random planet, you did the same with million times before, the game feels very repetitive and needs to be spiced up in this regard IMHO. Similarly i think some planets should have their own races/governments, basically as replacement for local militia with their own unique stuff...and you would be able to deal with them either in diplomatic or military way...some techs like currently Truce amongst Rogues would influence your ability to deal with them...
obviously for hardcore multiplayer these things would be possible to turn-off, to reduce the unwanted randomness, but for singleplayer/casual multiplayer i believe they would be great.