I'm not a representative from Microsoft so I will never claim anything with 100% certainty. But this is something that's been discussed for quite some time, from the very beginnings of the Xbox One. If memory strikes me correctly the system was always envisioned to be paired with either a controller or M&K. I agree that the best solution would be for the games that do support M&K to pool M&K users together, and controller users together. Melding them both together on the same servers will lead to anarchy.