I very much enjoyed Kazooie's final boss fight - no nonsense, exactly what you always were told you were getting, but you have to use everything you've learned thus far. It was the perfect end from both a storytelling and tactical point of view. My only complaint, which I would change with Ukulele, was that technically in BK you personally never defeated Gruntilda, just made it so that another could. I'd like to see Ukulele's protagonists actually succeed themselves.
Tooie's battle was interesting, and having Grunty pop up to ask questions added a comical twist, but it didn't really test your skills the way Kazooie did.
And it's been years since I last beat DK so my memory is fuzzy, but going by your descriptions above, I've got to stick with Kazooie.
Came to save my sister, stayed for the quiz show.