BOTH are great games. BOTH have their strengths and flaws. BOTH are absolutely worth playing.
My personal pick is Chrono Cross. I adore that game just a tad more than Xenogears, even if I acknowledge Xenogears has a much better story. I just prefer the visuals, world, music, gameplay, and charm of Chrono Cross more.
To me, Chrono Cross is the equivalent of a video game vacation to a beautiful location filled with beautiful music and beautiful characters, a play to see landmarks, historical areas, and observe the local wildlife.
Xenogears is the equivalent of a video game study on psychology and spirituality. It's very rewarding and its subject matter is very adult and deep. It's more "grounded" and tackles real world issues of politics, gender, race, religion, and the human condition in a fervent and meaningful way. It's far less "enjoyable" as a result, but there's more meat to it.
Due to this, I loved my time with both games, but Chrono Cross is the easier game for me to revisit time and again. It's the only game I have no problem just standing around doing nothing but looking at the visuals and soaking in the soundtrack and letting it transport me to some far-off location full of adventure, daring, and romance.