It had a better combat, more colorful graphics and fantastic stereo music. The plot was better (ie it existed) but also kinda nonsensically lifted from Laputa for a non-sequitor ending.

But mostly, they're just different games. Fundamentally, Zelda plays as a puzzle and exploration game. Crystalis didn't quite do that. Instead of maps and puzzles, you had mazes of passages, and a few town puzzles. Instead of exploring for heart containers, you grind levels by wandering around the wasteland killing anything that moves.