Banjo Tooie is my all time favourite because it ticks every box that I can think of for a good game.
1. Fun
2. Endearing characters
3. Imaginative
4. Good level design
5. Varied gameplay
6. Humour
7. Good camera control
8. Yellow-fuckin'-shorts
Plus, I'd say it can easily take the title as best game sequel ever. The game starts with EVERYTHING from the previous title and was built on from there. Not like other games where you end the game with a million billion magical spells or super powered weapons then start the next game with absolutely nothing to your name (read: the Zelda effect).
Banjo Tooie starts with every ability from the previous game and adds in twice as many new ones including fine tuning to previous abilities. The graphics improved, the game world was bigger and more diverse and most of the characters from the previous game returned. World exploration became more rewarding as you could discover new hidden abilities i.e. the breegull bash or dragon kazooie.
Plus, it was a Rare title from the N64 era of Rare. Amongst a stellar list of titles like Jet Force Gemini, Goldeneye, Perfect Dark, Banjo Kazooie, Conkers Bad Fur Day, Donkey Kong 64, Diddy Kong Racing and Blast Corps, Banjo Tooie more than holds itself up.
Basically... Banjo Kazooie was a masterpiece and Banjo Tooie took everything from the previous game that worked and added hundreds of other things.
I could rant about this game for ages, which I kind of have done already.