The Dread Lords tutorial, err, campaign poimted out the need for a solution to the problem when a superior force hovers over your planets picking off individual shps as they come off the line.
The soltion I found was the russian winter defense.engines are small and cheap. put a lot of them on your ship. when your ship is built, RUN AWAY!!!. Okay, that sounds like the french defense...
Anyway, that hulking fleet can't do anything without transports, and since the AI doesn't like to protect its transports, fly around and pick them off as they approach. Of course it is nice to have 1 or 2 tiny ships amped up on recon and speed to dart in-look for transports-call in your hiding fleet-dart out, because you don't mind them dieing on the rare occasion that they dart too close to the enemy. Eventually your transport killers coalesce into fleets that can eventually launch a counter attack.
Did I forget to mention that rather than building capital ships during peace time, I am building speed 40+ transports with excess population and storing them in the corners of the universe? The point is, you never take on their assault fleets. When the counter offensive starts, go straight for their production capital. Sun Tzu would be proud.
Of course, this strategy would not work if the AI understood the power of speed 40 transports because they could invade you from their home worlds, but I think we are safe from that until GCIII coms out.