The battles

Here's a thought: how about a triangular HUD element that switched your selected ship's power from one subsystem to another (bit like in X-Wing, if anyone remembers that).

So if you tap it at the top, all power goes to the engines: you're faster, but your weaponry reloads and shields recharge much slower. If you tap it on the left corner, all power goes to weapon reloading. Right corner, all power to shields. Tap anywhere else for a mixture (e.g. dead centre for equal power to everything, or anywhere along the base for a balance of power between shields and weapons, with minimal power to engines).

This would allow you to play more of a part tactically, constantly adjusting performance in a fight. You could also specialise ships more - have a close combat ship that pushed power to engines and charged across the map, then switched power to weapons to blast the opponents out of space before they had a chance to react...