To be honest, I don't see a lot of advantages of having an engineer on a science ship, but if you do choose to go that route, you might want to try one of the more cruiser-like ships such as the D'kora or Nebula. They can benefit from your engineer hull healing abilities.

My general rule of thumb is to fly your character:

A) In a ship geared toward your class, because then you get synergy between the skillpoints you spend and your BOFF and Captain abilities.

B) In an escort, since this game has basically released an expansion edition called: Escorts Online