Phew. I was going to have it so that there were different 'scenarios' for each planet. Every so often during the story you go back to your ship. From there you'd be able to select the planets etc. The planet that progresses that story would have a normal end level event leading to it, but the other planets that have already been visited would have secret level exits. All up I would have about 10 .j2ls for the ship, and only one .j2l for each planet's 'scenario'. That way you would keep going and 'unlock' more planets as you go. Sort of like Ratchet and Clank really. The problem with that simple solution, though, is that you can't visit the same non-story planet twice in a row before moving on to the next.
I wasn't going to quite use 'missions' as such, except at certain points where you could go to another planet to get a powerup or something. It made more sense in my head, really.