That might be the problem, I certainly found I had problems with very powerful shields

I find that capital ships have a hell of a lot of power to charge shields with anyway, so the best bet is to give them moderately weak shields, which can absorb, for example, the main impact of a heavy bomb or the like but need to recharge afterwards, but which tend to fail under combined fire, that way it gives the ship a weakness despite the shields.
Of course, this technique may not tie in with what you are trying to do
Flipside
