I suspect the reason that satellite layers are not picking up sats anymore is because I made planets launch all their sats rather than keeping 50% in cargo meaning that there is probably no stock for the sat layers to grab and distribute. I can tweak the priorities for satellites though to get a few more constructed.
You're not seeing any carriers for the simple reason, none of the AIs are reaching fighter 2 tech, which would give them the carrier hull. It should be fixed in v0.93. At least I remembered to keep 50% of fighters in storage on the planet for use in ground combat or for carrier pick-up.
I have seen the AI send out a troop transport with troops on it to join a fleet but I'm not sure if it will follow a capture planet strategy. I'll have to investigate this and maybe edit some strategies to ensure ships break formation - I can just see it now with the cargo and repair ships in fleets being the leaders and the AI fleets fleeing in combat.
The retrofit with cargo bug is an SE:V issue. Although I think I need to tweak done the priority for colony ships. In all my test games, the AI has more colony ships than planets to colonize. Even worse is that it will send all the available ones to the same planet (SE:V bug again, but at least fixable in the scripts) and so on.