ORIGINAL: Eldiora
I really hope something is done with the balance, i can invade and take over a whole star empire with only troop transports without any sort of retaliation. You just need 10 fleets with 4-5 troop transporst in them each (200-300k troops per fleet) and then simply send them to take over the stronges enemy colonies. No real defence anything.
It would be slightly better if planet defenders would focus fire on troop transports (or just focus fire, period) and maybe disable them with EMPs, however I don't think there's any defence against a swarm of 50 troop ships. [X(] Except maybe some kind of slow-mo field and powerful area weapons.
The thing I usually use is one capital-sized troop transport full of crack troops, and a moderately powerful fleet to distract the base defences. It doesn't even matter if they survive the battle as long as the troops land.
Edit: I just tried something crazy. I added 100 Ion Pulses and 100 Deurasian Shockwaves to a space port, and it did terrible, terrible things to a horde fleet. It wasn't really cost prohibitive either, well under 20k maintenance. Would love to see something like that on an AI planet. Of course it didn't only destroy enemy ships around it, but everyone else too.