After playing another game for a while, I definitely see what you're saying about the strategic value of tying up ships on planets - but I think it's gone a little too far in that direction. I have a replay where you can see the AI repeatedly throwing away valuable ships (transports especially) attacking the same planet while doing no damage (the only effect is my defending fleets level up constantly). It allows me to get away with a strategy where I just hunker down with my planets moderately defended and focus entirely on research and manufacturing until I can build a ship they cannot even damage every 1-2 turns. If these attacks came in the form of fewer, more focused waves (stronger, bigger fleets composed of combat ships, then transports only if they succeeded in wiping out the defending fleet), they would be much more threatening, and render this "turtle bomb" strategy ineffective.
Also, one other thing I noticed - the hull auto-repair mods allow heavily damaged large/huge ships to fully repair in one turn (gaining maybe 300 HP) by safely attacking a weak target. That might need a nerf, or maybe repairing when stationed in a starbase/planet needs a buff - it would've taken half the game to repair it otherwise. The difference seems to be a little extreme, and with huge ships, the strategy of attacking a weak opponent after sustaining heavy damage makes them too powerful (in the little experience I have) in relation to the smaller ship sizes. You can wear down a fleet, but a huge ship is either dead or effectively 100% alive if it was designed with this in mind. Maybe a hard cap on HP repaired per turn (regardless of vessel size) would address this. (Or, maybe, I just don't know what I'm talking about as I've only played a few games so far - I'm wiping out the AI on normal, but I understand that 4x AI always struggles with resource production so that's basically easy mode.)
I don't see an option for attaching a save file here, but I can provide it if it would be helpful (along with specific turn numbers/planets to look at with specific examples of the AI attacking with weak fleets). Thanks again for making a great game! It's awesome you continue to support it after 5 years and that you take the time to talk to us directly.