Microsoft can already separate OS versus application registry storage, but only in cases where the application is stored in a per-user method. If you install an application with "all users" scope (Do you wish to install this application for yourself, or for all users of the PC?) the registry items are installed at the HKLM\Software hive. However, if you install on a per-user basis, it writes to a virtualized version of the HKLM\Software hive which is actually stored within your personal HKCU hive. A somewhat similar thing also now happens with DLL's; old apps would dump their shite-ancient version of some core DLL into your System32 directory and jack up half the machine. Modern file virtualization drops them into the WinSXS (side-by-side) system and Windows helps the app sort out which one they need to operate.
All of this started in Vista as a compatibility thing which was intended to die, but turns out it makes a lot of things more stable in the OS and has thusly been kept:
http://www.thewindowsclub.com/file-registry-virtualization-in-windows-7
I'm not a fan of building a single database for every single application -- what, I need a whole new registry DB for Notepad++? Then I need a new registry DB for Calculator? And a new one for my Chess app? For Steam? For the stupid EA digital software portal thing whatever it's called? And then for each game I install within Steam? How does this work for UWP? Actually, I think UWP does solve this in some other way but now can't remember.
Yeah, maybe we hand-wave off some of the complexity by saying we will "glob them together by category." What becomes the common denominator? Manufacturer? Well, Microsoft is going to dick you there. By work type? How do you categorize all the apps on this planet?
And honestly, this completely ignores the eighty brazillion extant x86 Wintel apps already on the planet which are compatible with and could/would/will be installed on Windows 10. If you allow those dirtbags a backwards way of still working, then NEW dirtbags will just continue being dirtbags and relying on the wrong, old crap way too.
I'm on board for the app separation vs OS, and Microsoft is already helping us out there.