Rare originally planned a Stop and Swap feature for the game. Items collected in Banjo-Kazooie
could be transferred to Banjo-Tooie
by pulling the Banjo-Kazooie
cartridge while playing and inserting the other cartridge. Some of the planned items included coloured eggs and the ice key. Eventually, the feature was cancelled as they feared some data would be corrupted.
Originally Rare was planning on having a 2 player mode called "Bottles Revenge" where one player would play through the game as normal and the other would play as Devil Bottle's and try and stop Player 1 from completing tasks. Player 2 would try and stop Player 1 by possessing nearby enemies and using the enemies unique abilities against Banjo. Unfortunately because Banjo-Tooie
was so far behind schedule Rare had to scrap the idea by deactivating it at the last minute.
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- In Banjo-Kazooie Kazooie insults Bottles by calling him "Jam Jars". In this game the mole who helps you (Bottles' brother) just happens to have that name.
- Sabreman, the protagonist of this Sabre Wulf, makes a cameo in this game. In the level Hailfire Peaks, he can be seen frozen holding the lost amulet right outside the train station on the icy side. Also, the combination for Superstash's safe is 1984, the year Sabre Wulf initially was released.