I think Microsoft playing ball against is an extremely safe bet. The only variable I'm curious about is how cooperative they will be for base game vs DLC.
Few companies would turn down the opportunity to be a Smash DLC character, with no doubt extra monetary gain to be had from direct transactions. This is the only means we've had Microsoft represented thus far, and on top of that is the factor of overseas communication. I have to imagine on that second front, most of the dirty work with Banjo and Steve is already done so it would just involve a few conversations and emails to settle. First part hinges on how much Microsoft cares about that extra $$$.
My prediction is that Banjo and Steve can easily come back on base roster - especially Banjo, if all the Rare content on NSO is anything to abide by. They really seem to value the idea of Nintendo elevating their legacy Rare content since this is where they will find their strongest audience. Minecraft is perhaps a hotter commodity, but Steve is genuinely that big to be worth handing over the extra bucks to have on day one. But much like Square Enix (presumably) before them, and with how many viable and popular Microsoft characters there are, they will continue to have a big presence through DLC cycles and will negotiate one or two new characters around the same time they settle the return of the first two.
And as I've stated in the past, somewhat controversially maybe, I don't see one coming back without the other. Banjo being virtual pocket change to bring back and having been such a highly sought after fan favorite, if relations with Microsoft are good I don't know why you wouldn't just grab him again. That's assuming Steve comes back as well which most people would sooner believe. Which again, outside of being a pretty complex character I don't see why not.