I like to think that most of the people who bash CC do so because they simply didn't get it.

The second disc was crap, yes. It's always bad when half the plot of a game is given right before the final battle, if only because it almost completely prevents any sort of emotional development from resulting from any bit of that plot. Most of the details given were completely irrelevant to the rest of the story or didn't even make much sense the way it was explained, but I distinctly get the impression that the developers were expecting to be given far more time to make the game than they received, which explains some of the empty shells of characters that one can recruit, the confusing plot, and the general "unfinished" feeling of the game.

I'll be the first to admit that CC could have been a much better game than it was. But moments like the Serge/Lynx body switch and the entire sequence in the Dead Sea more than make up for it, to me. Hopefully, if Chrono Break ever gets finished, it will remedy some of the ambiguities in Chrono Cross's story, but I don't really have any more unanswered questions about CC than I do about, say, FF7.