Except that Kamiya clearly has some right of refusal that overrides whatever Sega, or maybe even Nintendo has.

More likely I think he just was wary of the thought of a crossover, especially one in which he wouldn't have any modicum of creative control. He's very protective of Bayonetta, after all. Still, hopefully this regret ends up being strong enough to get her in what I hope is the inevitable PXZ3!