400 points is a very different story, since the fighter heavy lists get at least one more ship. That gives more flexibility in activating the squadrons.
The more ships = more activation is a real problem. I encountered that very problem when playing AT43 (also using alternating unit activation), the more units you brought the more activations you had, giving you a clear edge over the opponent. There were armies that could bring elite units only, so you faced 4-6 units vs 7-10. Back then I felt that there was a need for some kind of elite unit bonus, when you are finished with your units while your opponent still has a number of them to activate. We never came up with a good solution.
Armada has the same problem. Unless FFG comes up with some nifty upgrade card(s) to help the carrier fleet out I don't see how to fix that. With more activations than your opponent you can avoid to activate a ship that will bring you into bad position, until you are the only one left to activate.
I used to play ship only and was very successful. I just started to use squadron more now, trying to make it work. Against weak players the squadrons are incredible powerful, but if the opponent knows what he's doing it becomes an hard game.
Edited by Shaadea