Ok, so I havn't ran a game of RT yet. I am setting up a series of three linked campaigns going from DH, to DW, to RT. That being said, one of the issues I have with RT is the fact that when going planet side, it could easily turn into the Star Trek away teams, where Kirk brings, well, the most important crew members down to the planet.
You look at the careers, and there are a few that seem like they shouldn't ever leave the ship. For example, the voidmaster, we assume, is in charge of one of the major divisions on board, and the captain would never risk him. Same with the Navagator.
How do you justify including these characters in parties that leave the ship?