I've played both Kazooie and Tooie again recently, and if I had to choose, I'd say I'm firmly in Kazooie's camp.
Don't get me wrong, Tooie is great. I was amazed by how ambitious it is, by how far it pushes the boundaries of the 3d platform genre (in particular with Grunty's Industries), and by how modern some of its ideas are. It felt kinda like a proto-open world to me.
But I also thought that some parts didn't work too well. Both Witchyworld and Terrydactyland felt like a drag, I've found the amount of mini-games a bit excessive, and the 1st person shooter sections were just too much for me. Plus, there were some absurd difficulty spikes, like Canary Mary's 2nd round or that shooter section in Grunty's industries.
Above all, when I finished it, I felt satisfied, but also really tired and exhausted.
And then I've replayed Kazooie, and yeah. That one is just a masterpiece.
The pacing is perfect. Every level is just a bit more complex and difficult than the one before it. The difficulty scales up in a natural way. Gruntilda's lair itself starts to become more complex and iterconnected the further you progress through it, and the tasks you have to do to access the next level or to get the next jiggy get progressively more involved. The levels' themes are simpler than in Tooie, but still great. Freezeezy Peak and Click Clock Wood really manage to feel magical. Grunty's Furnace Fun is an unexpected and hilarious climax. The final battle with Gruntilda is one of the best final bosses ever, really epic and really difficult. The transformations are fun and don't overstay their welcome (I can't say the same for Tooie).
And last but not least, Gruntilda's constant rhyming is just hilarious.
To me, Tooie is a really great game. But Kazooie is a masterpiece, one of those games that only come out 2-3 times per console generation. That's the main reason why I want Banjo in Smash, even besides my fondness for the characters and their world, an accomplishment of this magnitude absolutely deserves to be represented in gaming's biggest crossover. It is one of the N64's defining games.