The difference between (ex) Mojang / Notch and Microsoft is that Microsoft is a big media company. They make content, that they sell. They are openly hostile to anyone deriving revenue from their IP unless its through some neatly packaged portal through with they get their cut. The existing EULAs on all their current gaming platforms, for example, only allows uploaded videos to be displayed alongside advertising as long as the uploader derives no income from the advertising whatsoever.
So, all those "lets play"ers who might be deriving a small income, and modders who are compensated even slightly via Paetron or AdFly links are going to wave goodbye to that soon.
Notch on the other hand, was perfect to remain in charge of Minecraft, ironically for the same reasons he doesn't want to. He was not interested in milking Minecraft to make even more of a commercial success of it. EULA teacup storms notwithstanding, Mojang was quite prepared to let modders, and twitchers and lets players make whatever income they could off the side, and tried quite hard to only exclude monetiziation that would have negatively impacted the "cool"-factor of the minecraft experience.
Microsoft has spent $2.5b on this. They are not going to be content to tinker with it for the cool factor. They are going to take the Minecraft name and turn it into a bright, polished shiny "product" for consumers to consume.
It will be good. So very good.
And those of us, who remember modded minecraft, when anyone could contribute a mod will hate every polished moment of the experience.