What I find bad for Banjo's series is LOG. Okay, they can do a game with Grunty trying to get ride of LOG's factory. And then? If in a next game she makes a new plan, LOG stops her with no problem.
About the other Rare franchises, Perfect Dark was about the very first Joanna's mission as Carrington Institute agent (the GBC game doesn't count, according to the N64/XBLA game), and she was just 23. There's a lot to say about her and Aelphaeis Mangarae.
Conker has even two sequel possibilities: either Conker searching for a way to revive Berri and get revenge on Weaso, or a game entirely based on Squirrels/Tediz war.
I have no ideas about Kameo.
And Viva Pinata should have a DLC rather than a sequel... unless it will be something completely new (totally new Pinatas, kinds of garden, etc.).
Jet Force Gemini works good as an alone game, due to the ending.