I always wondered this myself, so I asked a friend of mine once, who is both a fan and a musician, and this is what I was told--
1. Their harmonies. Not so much that they used harmony, but the specific harmonies used were unique.
2. Their modulations (changing from one key to another), both with regard to the timing of the modulations and the specific chords changed from and to. Many of Brian Wilson's chords were complex and not used by other pop musicians.
The Beach Boys' "Pet Sounds" heavily influenced the Beatles' "Sgt. Pepper". Brian Wilson was pretty bitter about not receiving proper recognition for this, at least not by those who were *buying* the records.
I'm still not so crazy about them, but this is what I understand to be the reasons why some people are.
Steven Matthews