More missions throughout the levels (not just at the top - spread out from 1-45 so that there's more options)
More ships (both Fed and Klingon side)
Klingon PVE (Episodes specifically - Exploration missions are nice and all; but Klingons could have some really interesting and different missions from the Federation)
Felinoid race parts for the character creator
Federation Melee weapons, more Klingon melee weapons too. (The Bat'leth is nice, but it's hardly the only weapon they've got!)
More content all around (of course)
More weapon types; including stuff that's a bit more adventurous (ex: weapons that take up 2 weapon slots on a ship, but are powerful enough to warrant it.) More skills of course too to go with such things.
The ability to choose which hardpoints my weapons use. That is - instead of having some ships fire Dual Beam weapons out of their nacelles, let me choose a different set of hardpoints on the hull to fire them from. Let me spread my Turrets across the hull, rather than having them all clumped into a Foreward or Rearward spot. (I hate that if I have 2 rear turrets for instance, they both fire from the same location; and that even if I have a forward turret and a rearward turret, they fire out of locations very close to each other)
Very Long Term (ie: 2+ Years out) -
Additional factions - Caradassians or Romulans, with their own PVE campaigns to play through and stuff to do.