You didn't use the Chrono Cross properly in the last Time Devourer battle. Remember the sequence of colours the Cryosphinx gave you in that riddle? What you're supposed to do is wait for that sequence of colours to come up (or make it happen yourself, but Lavos ALMOST casts spells in that order anyway) and then use the chrono cross after the six colours are used. (I think it's yellow, red, green, blue, black, white, but don't quote me on that).

Square did a crap job of explaining that you're supposed to do that, though, so I can see where the confusion arises. I had the same problem my first trip through the game

The entirety of Disc Two was a bit rushed, storyline-wise, I thought, but in particular the events right before and right after the final battle weren't given enough attention. (SPOILER)Lynx=Wazuki? That should have been bloody HUGE, but they glossed right over that one. gj square.