Okay, I hate to be the one to ask the apparently stupid question, but I'm going to ask it and spare all of us the difficulty. First, the idea of auto pilot is awesome. It was a big part of all of the WC games (Incidentally, when you use auto pilot in WC saga, will you see a panning shot of your ships in formation?) From the way you are describing it, one of the ways you are going to make trips to waypoints manageable is by adding huge time compression. That sounds great, but I think there is one potential snag in that game.
I can imagine myself engaging 64 x auto compression, and then getting shot to pieces because I was unable to gauge the right momement for reducing time compression to normal again. Maybe you have already worked this out, but is there some way you can set the time compression to return to 1 x whenever a hostile is within a certain distance (perhaps just on the edge of visual range for a bomber)?
Also, I think it would be awesome to be a part of a fleet battle taking place over the distance of several nav points. That way, you could clear an area of hostiles, and then take off for the next area where help is needed, all of the time seeing the other capital ships and explosions off in the far distance, adding a sense of urgency for getting there as soon as possible. Anyways, this last part was just daydreaming, but hopefully the first part of this post was useful.
Sphynx,
Verbum sapienti, o pluris habient, e o pluris scipient.