as most have said previously,
i'd like to see,
A) a story driven Campaign for each race, following the lore of the intro Vid, as i really enjoyed the small amount of lore that was given through said video.

A new race, but, as some have noted, i also believe this is already in the process due to the whole "vasari running away from big bad unknowns"
C) a larger fleet capacity / more capital ship slots, i don't see why, if i can control 3 systems and easily support the current 79%tax*or whatever the max is, it slips my mind at this point and stage*, why i can't have a larger fleet, sure this would lag out some people, but the option could be added as Extra large fleets or something along those lines.
D) the ability to import / create Your own logo for your chosen race / More colors, i would love a black or white color for my ships.(similar to that of homeworld2's logo / color scheme)
E) More ships / buildings / Defense systems for each race etc.
F) More or less a complete implement of the idea's listed in this mod; http://tgnforums.stardock.com/306295
I.E new planetoid types, Natural Disasters / Benefits
the ability to populate Gas giants via anti-grav platforms as stated in the mod.
i'd love to see all that implemented.
its a brilliant idea, and i find works really well.
this is one hell of a list but i thought i'd get all my bases covered in one go.
one other thing on my mind, "hero" classes, i think it will ruin certain aspects of the game... this is a 4Xrts... it brings up way to many balance issues when you introduce heros to a game - but thats just my opinion.