I do think, in a lot of ways, Banjo-Kazooie is better than Mario 64. The characters have way more personality, the worlds are clearly more defined and lived in (whereas a lot of the worlds in 64 feel more like abstract playgrounds), and the missions are more varied (Mario 64 has a lot of repeating mission types, whereas the only jiggies in Kazooie that are really repeated are the Jinjo ones).
That being said, the one major thing Mario 64 has over BK is kinda the point of contention: the fact that it has much more advanced and fluid controls. Banjo's movement is pretty slow and simplistic in comparison to the stuff Mario can do in 64. So going by that, I could see why someone would prefer 64 over Banjo.
So basically, Banjo did do everything better than 64...except, you know, the core mechanics/gameplay. They're both still masterpieces though.