Why not stop them at both, since Pendos etc have such good acceleration?
Would stopping the majority of MK stops for West Coast long distance trains at BY instead of MK really inconvenience that many people, as long as connections are still available? If your destination is MK, chances are, unless your destination is right outside the station, you will take either a bus or cab anyway, so for longer distance travellers, I can't see much difference in stopping at BY instead of MK.