Shard, I hear what you're saying about a good Pilot not being able to increase his ship's AC. But I wanted to make one observation from my (very limited) experience with this system. If you use the defense bonuses from speed as listed, the ships are already going to get a bonus if they are travelling fast. If you let a decent pilot beef this up even more, I'd say you run the risk of lower level characters not being able to hit anything at all. Especially at the early levels, the characters who are not dedicated pilots are unlikely to have Starship Operations and therefore suffer the non-proficiency penalty to all attacks they make.
After all, it is easy for someone to have their Pilot skill bonus FAR exceed their ranged attack bonus.
Again, I haven't used these rules extensively and I may be way off base. But it seems like characters under 5th level who aren't optimized for space combat are never going to hit a TIE fighter if I let the TIE add defense for being a good pilot.
Thoughts?