In fairness, CT's original ending (regardless which one you get) was...rather lighthearted. Its just "They say good by, some silly antics happen!" The new stuff sounds like it takes things in a completely different direction, being all dark and brooding, so I can't help but wonder if some of the disdain (is that the right word?) comes from that.
I do fundamentally agree with both the fact that Square more or less dropped the series after CC outside of this Enhanced Port, which is pretty dumb cause while CC was generally considered worse, I wanna say it was fairly successful and enough to merit another game in the series (and heck, professional reviews I seem to recall gave it obscenely high scores across the board. I know one site said "One of our only 10/10s!", Playstation Magazine gave it "Best RPG of the Year" when FF9 was in contention, etc. You could argue this is more proof to just punt professional reviewers of course, but that's a different can of worms, and missing the point), alongside how Square should NOT suddenly pretend CC didn't exist.
There are CC fans out there, much as haters may not want to believe it...big ones at that. The game getting a nod from a remake of its predecessor shouldn't be too bad, let alone one that tries to help tie up some loose ends between the games, thus make them connect better. Its a flaw of CC that it had such a fucked up plot; but a successful game is still a successful game, and they aren't going to pretend it doesn't exist.
I mean, hypothetically, if FF7 is remade, and the series starts nodding at the compilation in different ways (like some random NPC mentions Genesis as being a forgotten hero of the past, or the ending tacts on a "hey look, its Kadaj!" type thing, or they turn Zack's death into something closer to what it was in Crisis Core, etc.), would that really ruin the game?
...ok, maybe it would depending how heavily the references are, though, CC and AC were pretty sane that the references/allusions to wouldn't hurt much. Dirge of Cerberus meanwhile...>_>;