Valve has been making quality games (TF2, Half Life, etc..) but I'm worried that they might hamper the game's space engine.
Bioware would be my first choice. They have proven to be good designers for space games (KotOR, Star Wars Battlefront, etc..) and I'm excited for their upcoming MMO.
Volition (The fellas that did Freespace and Descent. As well as Summoner and Saint's Row) would be a good choice in way of skill, but they're a relatively small company ever since their breakup with Interplay. I'd like to see them do a Freespace 2, but I don't think they have the finance to purchase the rights from Microsoft, since they can't buy Freespace 3 rights from Interplay.
BioWare would produce an orgasmic sequel, I think.
EDIT:
NO WALKING PERIOD. I love the quick travel, click to talk function of FL. I like to get in, grab mission / repair, go. I don't want to search around for the NPC I have to find. Or, in case of multi, fight through a lag-blast on Manhattan to get to the ship dealer.
A test flight option, or rent-a-ship would be cool for fighters. Test the ship's feel before going in-game.
EVE Online's auto-flight function would be INVALUABLE. Now, this opens up complications like pirating AFK ships and powertraders, but when I think about getting on my trader now, I get sick.
I think it would be cool if Freelancer's 3d engine was more exploited. People still treat it like a flat-plane game in jousting and such. The only times that I have ever used the Z axis if I was SNACing or Smuggling.