Teams that stack many gunships only do so because the other team isn't countering them. Like many previous post have stated, scouts are a great counter to gunships. I've been in matches where the other team starts out with 3-4 gunships and by the end of the match there was only one flying a gunship. On my flashfire I look for them them at 20-30k m out and barrel roll behind them and burst them down. Many times I don't even use missiles because that causes them to barrel roll away.
Gunships are easy to play only if they aren't hunted.
Edit: I do agree that the ion cannon power drain needs to be tweaked. Barrel roll for them is fine. The CD could be extended a little.