What would be considered canon in the Pokemon franchise?
Canon usually refers to the original work rather than the most popular one. As such, I would imagine that the original Japanese manga is canon.

The other mediums can be canon as well; the anime for example is a very important part of the franchise. Stil, the manga would probably still take precedence.

Canon is a very broad term that can be as strict or lenient as the user who uses it, so it's hard to answer this question definitively.