I just finished my first 1v1, regarding capships. I did notice quickly they were far more vulnerable.
In Sins, I could just send one colonizing capship over to every single non-enemy non-pirate planet and know ingthat not a single point of hull damage would be taken was effective to me, so I could beef up the eco and Research at home, hell as soon as I had enough for a second one, killed my scouts and built the second one, and I'd be fine. You could go through a sins game against normal cpus without building a single frigate or Cruiser.
I was surprised at how vulnerable they were mostly because of the lack of battle regen which made them ridiculously op to start in the original. It's an interesting tradeoff, however when it comes to the player vs player battles in Sins 1 and there are multiple capships in play, a proper cap ship with a ton of regen was almost impossible to kill unless you held it down for minutes while it tried to run away. From my perspective dealing with them wasn't fun, and it was less punishing losing a group of Frig and cruisers compared to losing a level 5+ cap ship, now when there were four or 5 cap ships on the enemy side. It was just utterly painful You could focus down the level 1-3s but the others just had so much tankiness unless you had ridiculous overwhelming force.
I think the way things are now, Capships are more balanced supply wise compared to how they were in sins. I wonder if shield regen in battle might want to be reintroduced by default on all ships however, but I'm more than fine with no hull repairs in battle (Unless by ability of course)
One positive I did notice is, I always had the anti matter I needed when I needed to do an ability specifically colonizing. Expansion for me seemed to be limited more by economy rather than Cooldowns/Antimatter which I appreciated.