Sounds interesting. It seems I played a game a few years ago, (might have been a Star Wars game), with a similarity to your choosing of a ship, planet, crew etc. Do you happen to know what game it might have been?
I don't know of any exactly similar game but here is a possibility:
The Star Wars Old Republic game (a RPG by Bioware) has companions, a starship and fun space and planetary quests.
Startrek Online has fully developed crew missions and some planetary quests too.
(edit: I don't know much about Star Wars Galaxis however, which could also fit what you described)
These follow the "old" MMORPG formula, though I believe they are great games, they require a lot of focused time.