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.