I think they both are excellent RPG's, but in different ways.

Xenogears has the best integration of mecha in an RPG that I've seen. The characters are complex, the plot is involving (and a little confusing at times), the battles are interesting and the music is nice.

Chrono Cross has a huge cast of playable characters (which means less depth but lots of options), an interesting magic system, and good replay value. Fast Forward is a godsend! I wish more games had that option. Nice music as well.