To expand on the "lots of targets" idea, go ahead and use fighters - but launch them in Groups of 1. That's right, give him hundreds of targets to shoot at with his Talisman-armed PDC... a few (hopefully more than a few) are bound to get a shot in. I might also recommend engine destroyers, although their usefulness is now limited somewhat because they no longer skip shields. But if the enemy's engines are gone (and he doesn't have Quantum Reactors yet), he can't move and (without supply storage) can't fire his weapons...
And, as someone else mentioned, start destroying his stars. I prefer turning them into singularities, just to add insult to injury. Kinda fun to watch the enemy deal with multiple black hole systems in a row...
