I can't remember the exact aspects he didn't like, but he did say before that GC2 is not a classic, but WOM is. Obviously the marketplace disagrees. That's got to be tough when what you like in a game and what the rest of the world wants are two different things.
IMHO some aspects of the economy were a little screwy. I didn't care, personally--it's a game. Things like the population had no bearing on the productivity of the planet, the taxes were a function of the square root of the population (??), and production had to be matched with 1bc of cash; those were a bit screwy. Ships' defense was screwy. Fleets couldn't defend planets. That's what I think stardock might not have been entirely happy with.
What I would have liked, personally, are more planet tiles types and more fleshed-out invasion tactics. And I like planetary bombardment, but I think there should be a limit on how much bombardment can do, which increases with technology and decreases with planetary defenses. Kind of like how in Civ4, a catapult could only do 15% collateral damage, but artillery could weaken it by 50%. And I think your placement of improvements on planetary tiles should matter, e.g. a factory surrounded by 4 other factories gets 20% output increase. Galciv2 was kind of a free-for-all--you would just randomly click on a tile to put anything anywhere.