Since ships are technically toons, I'd like to see Cryptic put in a save configuration button (like they have for uniform slots). The bad thing about swapping out ships is reloading the BO's and reconfiguring everything again.
If they did that, the game would be a lot more fun for me. I could alternate my engineer between the TOS Enterprise and the Reliant Refit, science officer between the Oberth, Nebula Refit and Intrepid Refit. I would also alternate my KDF sci between a bird-of-prey and the carrier.