Banjo-Kazooie 3 Rumors 

Rumour Three: Banjo and Kazooie travel back through time in pursuit of the witch's giant T.I.T.
Grunty drives her Time Interfering Truck back to before the bear and bird met. The duo must reintroduce themselves and relearn everything they know in a completely new way!

That sounds the most likely as then you introduce Banjo to a new generation, whilst at the same time making the older players happy. Also, they could teach themselves Wiimote actions and new things learned in Banjo 2 that they can then have earlier on and be better at by the time they get back to the Banjo 3 timeline.