Here is a post with the letter from Notch.
http://www.theverge.com/2014/9/15/6151941/minecraft-mojang-notch-goodbye-letter
It sounds like Notch didn't like the responsibility of such a big success. He had a great idea, got the ball rolling, hired more folks, kept the ball growing... I can't fault him for deciding "okay, I'd rather someone else take this over now." I'm sure there are other options, though. When you're the boss and primary shareholder... can't you tell the company what and how much you want to do?
But Microsoft? They're in charge now? I'd readily admit it's pessimistic, but I'm pretty skeptical here. Look at their current projects -- are they about quality, or profit? True, not many companies could play with 2.5 billion dollars, so there aren't many options. Sadly, Notch said he discovered, and disliked, that he wasn't in touch with the fans, but I see this as giving it over to someone we don't even know the address of, in terms of fan connection.
I really wonder what is going to happen with the new API that Mojang was "working on." Microsoft doesn't strike me as historically interested in providing versatile interfaces so others can modify their software. The mess with Bukkit is a little confusing to me... but even worst-case, if that was crash-and-burn, the API should have made it moot. Now I have serious doubts about that future API.
Sorry, I just got a call and I have to go pick someone up, so I can't polish this or elaborate more at the moment.
tl;dr I'm nervous.