I think transports will be a bit too cheesy in the near future, especially with all the buffs that they just got. Now that loading is done per fleet rather than per ship, maybe a way to reduce cheese is to have it so that after an unload command the fleet can't be ordered to load until after 5 seconds.
There's a specific change since the first game that makes transport cheese very attractive, ships continue reloading while they are inside a transport. You could do a hit and run in the first game by unloading, waiting 1 frame, then loading, but you couldn't endlessly repeat it to destroy things while taking very little counter attack.
Right now with how tanky transports and golems are, it's very attractive to let your transport's +1,000,000 hp absorb most of the AI's attacks and just unload every 10 seconds to fire off a volley.
I had kind of been braced for something along those lines. I'm not sure what the ideal solution is, but I really was not a fan of how inconvenient transports became over the course of the first game's life. As we fought cheese, they got slower in unloading, and various other things that I just felt like were irritating. I'd like to avoid that here, but I can see where the cheese definitely would come into play.
On the subject of reload timers counting while loaded, that's something I feel like is important (not that you suggested changing that) because otherwise people have to be sure all their ships are in an ideal state before loading them, if they are using them properly and taking them on a long trip and then unloading them. Having some ships still in the middle of reloading their guns when they dismbark would be a definite PITA.
As far as making transports more fragile goes, which you again didn't suggest but kind of alluded to, obviously that doesn't work with Arks and Golems as you noted, and even for regular transports its something that I feel like would mess with the flow of a lot of battles by not letting them keep getting reinforcements from factories if they get crippled too easily, etc. So that tankiness is definitely good.
You didn't bring this up, but I'd already been thinking that the ability to move your ships really quickly (triple speed) from one part of the planet to another is super powerful and might lead to some interesting abuses.
This also has the possibility of "dodging" long-range incoming shots from enemies that fire from far away by popping your ships in and out of the transports repeatedly, causing them to get away from incoming fire and not take damage, then be right back out where they can return fire.
It was possible for people to do something similar with wormholes, although a lot more tedious since you have to move your view or at least go to the galaxy map. Part of how we solved that was with a "just entered the planet, can't do anything for a moment" status on ships coming through wormholes. It makes them sitting ducks for the very first little bit out of the wormhole, IIRC. Though we've adjusted that so many times I can't remember what the exact current mechanics are, to be honest. Since I'm not trying to cheese things, I don't tend to notice the exact stuff on them there.
Something along those lines, with a stun on ships that just got unloaded from transports, might be good. Maybe the stun is longer if they were just put into the transport? It's 10 seconds if they were just put in there, or down by 1 second for every 4 seconds they've been in the transport, perhaps? That way there's no stun at all if you're moving between planets (and taking 40 seconds to do so, anyway), but if you're popping your ships in and out repeatedly they'll literally be paralyzed by it most of the time.
I guess letting them move would be ideal, but not go through wormholes and disabling all their systems including cloaking... or maybe just weapon systems? I dunno.
Thoughts welcome!