Talenn, have you looked at
my Proportions mod yet? One of the main points (besides slowing down development of colonies and research) is to provide large numbers of valid design trade-offs. Small ships remain viable. Fighters and troops become almost necessary. Trade-offs appear between fast ships and long-range ships, firepower versus protection, quality versus economy, and so on.
I have adjusted the weapons and abilities around to make more variety of effective design. I had started a massive overhaul of the weapons and technologies, but these had to be cut from the original mod design for time reasons before the Gold deadline - just the manual work of re-doing the weapon entires was what took the most time, but eventually I might get around to it.
I too decided the AI had to come second. I actually have managed to get it to mostly work, but it takes way less time to set up interesting game changes that it does to tweak the AI to use them.
PvK