Raid Starships II/III - I routinely use them to drastically reduce the combat effectiveness of an AI planet that I'm trying to take over, and only rarely do I send my main battle fleet in until I've done a guard post cleanout. And even when I'm not trying to take a neighbor planet over, I'll still go over and whack the guard posts and any warp gates present.
Scouts II/III - Have you tried getting MKI scouts out more than two or three worlds beyond your territory? Maybe even clean out some Tachyon Guardians on nearby world? Good luck with that. Once I secure an initial group of worlds, I need the info so I can make a beeline straight for the AI homeworlds (stopping off at Advanced Research Stations/Factories on the way). To do that I need large groups of scouts that can survive very many jumps.
Fighters/Bombers II/III - The fighters are to deal with bomber waves and take point on most assaults, the bombers are to deal with things that require bombers (force fields, spire shield posts, astro train stations, etc).