Nothing will change as a result of this.
Lots of that is speculation on what I hope Microsoft does with this, namely adopting Apple's marketing simplicity and control of the user experience.
For example, Microsoft is permanently enjoined from restricting OEM crapware preloads. OEMs are allowed to preload whatever they wish on top of Windows.
However, it's perfectly fine for Microsoft to bundle an app store -- so long as an OEM is also allowed to load its own app store. (As Lenovo is doing.)
As for Windows RT and Windows Phone, Microsoft can do anything it wants. When the news came out that Windows RT would only allow Internet Explorer and would only allow programs to be loaded through the app store, the EU competition commissioner said in an interview that he saw nothing wrong with it.
That's because the antitrust case defined Microsoft's monopoly to be over x86 operating systems. Windows RT and Windows Phone run on ARM. What's more, Windows RT and Windows Phone do not have anywhere close to a monopoly of the tablet or smartphone markets.
There may be some tying issues, but branding is not a form of tying.
A good guess is that the enthusiasm at e.g. Samsung for making Windows Phones have gone down quite a bit...
Windows Phones seems to be an internal Microsoft thing now, Xbox style.
It's probably part of their IP licensing deal about the secret patent list Android violates. They pay less per Android phone if and only if they build Windows Phone devices.