Watching the new Nuts and Bolts videos I belive I have found out all levels that were planned for Banjo Kazooie.
Spiral Mountain
Mumbo's Mountain
Treasure Trove Cove
Clankers Cavern
Bubblegoop Swamp
Gobi's Valley
Freezeezie Peak
Mad Monster Mansion
Rusty Bucket Bay
Click Clock Wood
Fungi Forest
Hammerhead Beach
Mt. Fire Eyes
Glitter Gultch Mine
Witchy World
I know Glitter Gultch Mine is fact and I'm pretty sure about Witchy World. If you want proof watch my youtube video:
http://uk.youtube.com/watch?v=rh282pJ4W6c
The only thing I'm wondering is where the last five were going to go. I'm almost positive Mt. Fire Eyes was going to go where Mad Monster Mansion is, it's pretty obvious with the lava and stuff.