Jason:
From what I understand, 'Medium Bonus' is giving the AI 3x Research and Production. That is a helluva bonus!
Late's game has no bonus so I'm sure it simply doesnt have the resources to amass ships as quickly. So it sends them one at a time and they die. I've seen it incessantly too with No Bonus.
The way I have the AI tweaked in my set, even a Low bonus results in the players being wiped out unless they resort to 'cheese' tactics like the missile dance. My solution so far has been to give the AI 5000 RPs while the players take 2000. This seems to give them enough of a boost without giving them a huge resource and tech edge...ie not even playing by the same rules anymore.
Late: Try the 5000 to 2000 RPs and see how it goes. Also, make sure and grab the AI mod pack. It adds some really tough customers to galaxy!
Talenn