I prefer Banjo-Tooie because it has more diverse gameplay IMO. You basically start off with everything you learned in Banjo-Kazooie so you have more abilities in Tooie. Both are excellent games though, and my preference is very slight.
I love both games to death, so it's hard to choose. I played Kazooie first and then Tooie. The first feels more original, but Tooie expanded on it so much, and in all of the right ways. Tooie defines on what a sequel to anything should be.