Arrow Gamer
America's Dictator
No more heroNESes til at least one dies.
Or, potentially, you need not have forced them ALL on one ship, but had three or four ships that they could choose from. And move between, if they so desired.
Problem would be that, then, when the reward was a ship mod, only the ship owner would win that. Mayhaps it could be everyone having their own small ship, and the ships could be connected with each other, to create a bigger, more powerful ship. Would provide for the combination of independence and companionship that maybe players would like. And each person could mod their ship the way they wanted.
Maybe something where you need at least 2 to do/start most missions (or official ones). Also maybe there is a chance of miswarping, with more/better ships working together they can warp more successfully.
I have just become a fan of AH.com. Curse you all.
And part of the reason why AH.com seems to work might be that they don't always have all the characters involved. I think allowing players to split up as desired would help any theoretical third incarnation.