I think Ben Folds is underrated for what he's produced. I think people who listened to him in college write him off as being frat-rock but his stuff is actually super interesting, the more you dig.
Ben is a master writer of story-driven songs, with a very wide range and top-notch musicianship. There is definitely a similarity.
Perhaps you're not familiar with his full catalog?
That said, they are leagues apart. It's like claiming Eric Clapton is as good as a guitarist in some shitty bar band.
Perhaps you're not familiar with who Brian was and what he's done.
Seriously though, it's often fraught with peril to try to compare two artists directly, especially across time, styles, and genres. For me, I just try to weigh how much enjoyment their respective catalogs have given me, and I've enjoyed the hell out of both Ben Folds and Beach Boys records. It's all good.