Can't we just have a phase in-between the ships and squadrons just for flotillas. Like a support phase or something. Time to repair off some damage on your capitals, mess up others dials for next turn, and still move some squadrons before the squadron phase comes around. Then the ship phase truely is for fighting ships, and flotillas are still useful but not annoying.
Then if they ever added some other support ships like flotillas they could also slot in here. And it'll be like a sub-ship phase.