It took some time to decide whether or not to post this as a suggestion or a bug, but I eventually settled on the latter. Given our 1300 AI progress, the idea of only having 20-30-ship raids seems laughable. Having said that, they tend to be accompanied by two or three Mark III starships, all of which are too fast to be even minimally damaged by our gate defenses. The only things that can keep up with them without being obliterated are the teleport battlestations (by micromanaging them), which since the starships having their health quintripled, do so little damage that it has grown to the point that by the time they've been destroyed, so has most of that system. Would it be possible to increase the number of ships and decrease the number or level of the starships coming through?
On a related note, why is the Flagship faster than the Light Starship? That just seems so odd to me...