Agreed. I could only see Sakurai adding Master Chief if he wanted to go the "icon of gaming" route, in this instance, being the face of Xbox, as it would certainly be a risk when it comes to Japan, a demographic they care more about. And I just personally don't see Sakurai picking characters in that way (and, I think Nintendo's picking the characters, so I find it even more unlikely, unless MCC for Switch is true and they want to have a connection there). If they do, it would be purely a pick for Western audiences, knowing that it would blow up big (bigger than Banjo & Kazooie, since they're often associated with their N64 games, whereas Halo is purely Xbox).
Though, I think that Master Chief has a higher chance than Minecraft--from a character perspective, there's more to Master Chief as a character than a Minecraft character. Though, I don't want to re-open that old debate, especially since I'd be fine if either one got in. My personal hope is for Crash, if there's a Western pick.