I posted something similar in another thread. Over the weekend, I made a Mobula build that I really like -- love in fact. There isn't a lot I can see that needs changing. At the moment I think the Mobula is pretty balanced. I have no problem dealing with Junkers or Galleons. Pyris and Goldfish can be a problem unless I can work on em from long enough out or get the right things knocked out.
I'm not saying I have unlocked the mysteries of the Mobula, but I can say for certain that most builds I see are a confusing mess. The layout I have has a whole lot of pain to deal out and isn't hard to engineer at all.
My biggest tip is to not repair until what is attacking you is dead. The only real advantage the Mobula has is the 3 guns it can easily get on any target at just about any range. Don't give that up to die on the way to the hull or balloon.