I have no earthly idea why this entire situation interests me so much as I don't care about Fortnite and I've probably watched less than 5 minutes total of him (no real opinion of him), but it just fascinates me seeing the "business" side of streaming games. I actually think it makes sense from almost every angle.
From Ninja's POV: He is still a HUGE deal, but every Twitch metric you can judge him by he is MASSIVELY down from a year ago. He's not even coming in close to pulling in similar #'s from the past, he streams much less, and his ability is not "championship" level which he was considered "elite" before the competitive scene hit, so his "mystique" took a sizeable hit.
Honestly, his "future" on Twitch might have been ugly for him. He's basically a one-game streamer and he's not near the top when it consistently comes to drawing in viewers and his ability. Also, seems to be doing more "business" type of things so he has less interest in grinding it out all day on Twitch. Moving to Mixer, his #'s will hardly be held to the same microscope that they might have been at Twitch and he can do more "business-sy" type of things and be more of a brand ambassador (he'll probably be a huge component of the next Halo reveal/coverage/preview/etc). Also, probably got a buttload of $ for it, which is pretty savvy move at the "twilight" of the peak of his streaming career.
Microsoft/Mixer: I kind of look at this from a sports POV where a small market team massively overpays for an aging free agent. That makes it sound worse than it probably is, but the ripple effect of people talking about their platform and whatnot just from paying him is probably well worth it. The $ spent was more of an advertisement for Mixer rather than an expectation of what they expect to get back from Ninja's streams. Probably well worth it to make that splash and show people that there is an alternative to Twitch.
Twitch: I honestly don't think they care that much. Ninja is a "big deal," but nowhere near what he was a year ago and there's a never-ending supply of gaming prodigy 15-year-olds who will vie for his audience and probably a vast amount of his subs were Twitch Prime which obviously won't carry over to Mixer thus locking in people to the Twitch platform.