I'm thinking of changing the NPC CO before the next story arc kicks off (see Romulan Crisis thread). Up to now, the CO has been a bit of a Picard and some of the PCs actions have got a bit outrageous but it got the job done so I didn't have the heart to crack down.
The new CO I think is going to be different, I'm thinking of Humphrey Boggart's Captain Queeg. The only problem is that what I don't want is a Caine Mutiny...any ideas of how to head this off. The simplest solution is not to do it, but then I want the PCs to stop their outrageous solutions - I know its part of the job but it can get to be quite a hand full. I had to stop a game once for half an hour to think through their latest spanner in the works.