Just started using transports last night, and I burnt through a level IV planet with about 1/3 the effort I felt it should have taken.
They're a complete game-changer, and they're essential to gameplay as they currently are. With 4 million HP, I can wormhole in, transit an entire sector to an ion cannon, use 600 Tech-I and Tech-II ships to blow the special ops post that it's protecting, load back up, and wormhole out losing maybe 1/5th of my entire force.
After doing a few more ludicrous things, like crossing half of known space to take out a datacenter just for the hell of it, blowing a command center in a dead-end level IV planet that had built up to about 3,000 tech-IV ships into a flypaper system that bulked my fleet by about 500 level IV units, and several other sick and sadistic things, I came up with a few recommendations.
1) Transports are basically big, empty volume that stores ships. They don't have 4 million points of armor covering the entire thing. Ships that are inside should take damage (spread out over the entire thing) at the same rate the transport itself does.
1.1) This should extend to ion cannons. An ion cannon that can single-shot a normal ship should single-shot a ship inside a transport, or do the equivalent.
2) Transports need to unload slower. They should need a beachhead to expand into, as opposed to BEING a beachhead.
2.1) It might be worthwhile to explore an "Assault Transport", "Raid Transport" or "Breaching Craft" sort of unit that takes the place of the guerilla role. Smaller unit capacity, lower expense, same fast speed and without the "holes in the outside damage things on the inside" nerf
2.2) Add a "Fleet Transport" that moves relatively slowly but can haul 500-1000 ships + a flagship/Light Starship for those long-distance delivery runs of an entire fleet.
2.3) Assault Transports should not be able to hold starships, but bigger transports should be able to. Having to wait a half hour for your dreadnaught to transit five planets sucks when the rest of your units got there in thirty seconds in the transports.
I would also categorize them as a starship and build them in a starship shipyard.