Ugh. The two of them cannot be compared on the same level, therefore there's no "better or worse".
To begin with, Chobits is an comedy ecchi with some drama. Chobits is about fuzzy feelings, and cute things.
Fruits Basket is a comedy-drama, its got a dark side, and a light side. Fruits Basket oscilates between both, some chapters are about funny situations, while others are about traumatic experiences.
Chobits spins mainly around two characters. Fruits Basket, as far as I remember, involves more than just two characters. Fruits Basket has a bigger action portion than Chobits (Chobits barely has any action at all).
I also got the impression that Chobits, while obviously having ecchi moments, was targetted to a more "mature" audience because of the suggestive themes.