Many of the decision trees probably need to be tweaked now that defenses weigh so much less:
HP vs Capacity = for almost all ship sizes you get much more bang for your buck with 10% capacity vs 15% hp, as well as flexibility to go offense instead of buffed defenses.
Defense size vs Defense Bonus is a null choice now that defenses are 2 mass (.2 reduction in size vs 10-20% increase in effectiveness is a no brainer, there is also an iconian tree decision that also asks this choice, probably others as well).
Its just an observation, but it still seems beams are the best weapon technology. I'm not quite sure how to objectively test it, but whenever I delve into misses or kinetics I lose fights / ships that I dont think I would have with beams.
The Happiness and Food % bonuses sections in most trees may need to be rethought, they cap out at 50% boost in Happiness or Food, but in almost all planets its better to just have another farm or happiness buildings. Uber planets can benifit, but its rare. The first two levels of the tech 10% and whatever the next one are should never really be built.
Certain buildings like the Embassy and Molecular fabricator (iconian tech) can be rebuilt once the next generation model is complete. Im guessing that is a bug. The molecular fabricator line (capps out at industrial) seems a little lackluster for a civ special building.
Ship ranges feel pretty high, especially as you progress down the tech tree and add the hyperion buildings. I rarely build life support on my warships as it's really not needed. The AI always adds a bunch, when it really only uses them to sit in my space instead of it's own, or generally clump together in some distant part of the map rather than defend its own territory ^.^ So many times I've seen one AI chomp another AI to pieces because the AI getting owned has parked all of its ships deep into my territory, while the other AI gobbles them up. Doubt you can do much, other than alter the building plans, and nerf life support and force the AI to work more locally (which may be a good thing?).
A number of races seem to churn out high attack no (or low) defense ships. I usually do the opposite and cut through those ships like a knife through butter. This is especially prevalent during the early to mid game. Most ships I see are weighted very high on offense and have hardly any defense. I'm pretty successful in employing the opposite.
Have you updated the overlord ship plans with the mod? I don't even know what to do with these things, they are so awful when the event pops 
I'd love to see a pass over of the galactic events. I'm not sure if you can control them or not, but some (ie doubling of engine speeds) are pretty silly overpowered.
Has anyone else seen fighter modules on starbases work? Since the last version of the mod was released they do not seem to add any fighters to my bases.
Can't wait for 1.4 and the new AI, as I do feel the bonuses you took away from the AI the game went from pretty challenging to fairly average / kinda easy on godlike. The dangerous AI's overbuild until they nearly collapse (three to five hundred low tech ships) which stops them from colonizing and growing, whereas before they seemed like they could do both at once.