One thing that is missing for Captain Flip compared to other games is interaction between players. Other than taking the map from each other it's pretty much a solo game, so the ability to flip tiles on other player's boards would feel like a big improvement, and add to the strategy as you'd be paying much more attention to how your opponents place their tiles. Trying to find extra gunners to take them over their limit is one way it would be useful, as is turning over their more valuable tiles to reduce their final score.
I also like the idea of introducing bonus points or effects for certain combinations of crew members. For example, if you place a Gunner in the same column or row as a Parrot then the Gunner shoots the Parrots and they get flipped. There could also be penalties applied, for example if you play a Navigator and you have no Cartographers (amazing how frequently this seems to happen in the early game!) then maybe you lose a coin (assuming you have any).