As much as I loved Banjo-Kazooie, to me, Banjo-Tooie takes the cake =)
I know some people think the worlds are too big but this never bothered me, I loved exploring Mayahem Temple, Terrydactyland, Hailfire Peaks etc.
The main reasons I prefer Tooie are the following :
- Interconnected worlds : I simply love the facts the worlds are interconnected and that by doing something in world A has consequences in world B (ex : breaking a rock in Cloud Cuckooland fills Dippy's pool in Terrydactyland, etc.)
- First person segments : as annoying as the can be (especially cleaning Grunty's Industry sewer from Clinkers), I loved this implementation (feeling like James Bond but with a living Breegull as a gun

)
- Boss battles : To each world, its own boss and though they might not be the toughest, they still represent a challenge.
- Playing as Mumbo : even though his role was short, I loved roaming around as Mumbo, watching him cast spells and listening to his chants
- Humba Wumba : 'nough said! Humba's awesome

My only complaints : Grunty stopped rhyming

(damn you Mingella and Blobbelda) and ugh... Canary Mary... (my thumb still remembers her...)