Well, this is quite the unexpected development, so soon after the announcements of Mega Man Universe and Legends 3. o.o Both looked like Inafune's pet projects, after a long drought, you'd imagine that he'd be more excited to focus on those.

While I think that most Mega Man news sources focus too much on related Capcom content instead of sticking with the core of the franchise, I'd dare say that this is worth of a news post. After all, Inafune has been there for the series since early in Mega Man 1's development, over 20 years ago.

With that said, I won't especially miss him. He's done good things with the franchise, but it also feels like he hasn't been much in control of it for a decade. This could either slow down future game releases, or give a new dynamic to the series; I'm willing to take that gamble. As to guess for the real reason of this move, I'd say that, perhaps, he realized that he wouldn't get as much control as he'd like over the two upcoming titles. This would explain the odd timing of this announcement.

I'm worried about Megaman Legends 3. This guy was involved with many great Capcom games, especially in the Playstation era. It's sure a big change in management. But, no one can stop a guy from following his heart. I hope in whatever he does next, it turns out great for him.

tl;dr.

There's a gem here: "KI: That's absolutely right. So told Capcom that I'm leaving to start my own company, while still contracting with them, continuing with titles already underway and follow through with their plans. If that was acceptable, I wouldn't be able to work with any other publishers, but I'd have been able to finish what I'd started. However, that wasn't possible. I was told, "That won't be necessary.""

Or, the short version:
Inafune: Hey, I'll help you with the ongoing projects.
Capcom: No thanks.

They might be painting it as a quiet departure, and it likely is in some ways, but I'd bet that the relationship had been strained for some time. This goes to show that Inafune, as an individual, cares about his staff and the fans: he was ready to stick around to tie up some loose ends. Ultimately, the company decided to do without his help. This only reinforces the feeling I wrote about earlier: "it also feels like he hasn't been much in control of it for a decade" Even now, at the end, he's being pushed aside.

Figured I'd update this.