After spending well over 8 hours trying to work through this issue, including a reasonable amount of Google searching, it seems to me that Microsoft has royally fucked up the Microsoft Store Windows 8.1 Upgrade for Windows 8.0 users. And now, I'll explain it in a little more depth...
For anyone who needs/wants to reinstall their Windows 8 (RTM), then activate with their license key, then install the updates needed (KB2871389 and KB2917499) to get the Windows 8.1 upgrade from the Microsoft Store and upgrade to Windows 8.1, you're in for a bit of a shock if you need to run applications that need the .NET Framework 3.5 (or 3.0 or 2.0) Feature that's normally installable via either the Control Panel or a particular invocation of the DISM command.
If you try and install via Windows Update, you'll be presented with the following error message:
Windows couldn't connect to the Internet to download necessary files. Error code: 0x800F0906 (which, of course, is bullshit if you've got a functional Internet connection - this is an erroneous error message)
If instead you try the DISM way, you'll see either the above error code or the following:
•0x800F081F: The changes could not be completed.
The reason for this, it seems, is because downloading the Windows 8.1 Upgrade from the Microsoft Store gives you the latest slipstreamed install of Windows 8.1 with almost all current Updates and HotFixes. Normally that would be great as it means that you don't need to bother performing a boatload of updates after installing the Windows 8.1 Upgrade, except that it seems that Microsoft has chosen to include in the slipstreamed Upgrade, HotFixes KB2966826 and KB2966828 (see: http://answers.microsoft.com/en-us/windows/forum/windows8_1-winapps/cant-enable-or-install-net-framework-35-in-windows/2f221b25-8d17-421f-8c37-1fed61649b4f) which are .NET 3.5 updates, meaning that until you uninstall these (which you cannot do if you've installed the 8.1 Upgrade from the Microsoft Store) you are what's known in the trade as SOL if you want to install .NET 3.5 (including 3.0 and 2.0) in a newly installed Win 8.0/8.1 from the Store.
As mentioned in that answers.microsoft.com thread, if these have been installed as part of the regular Microsoft Update regime before .NET 3.5 is even installed, it is a simple enough task to uninstall them, install .NET 3.5 and then reinstall these updates. This is not the case with the slipstreamed Windows 8.1 Upgrade from the Microsoft Store as these updates seem to have been slipstreamed into the installer, meaning that they don't show as updates that can be uninstalled, therefore they can't be uninstalled, therefore you CANNOT install .NET 3.5 on this system - that leaves a lot of software that won't install nor run properly.
Out of interest, this thread also details issues with these updates - so it isn't just on Microsoft's own site that this issue has been discussed.
I have found - as expected - that even if you install .Net 3.5 in Windows 8.0 before performing the Microsoft Store upgrade to Windows 8.1, Windows 8.1 is installed with .Net 3.5 uninstalled. As I said, I expected this behaviour and would have been rather surprised if this had actually worked.
It seems to me that the easiest fix for this is to re-release both of these HotFixes with better pre-requisite detection and also rebuild the Microsoft Store upgrade image so that these two HotFixes are not included, or alternatively, fix the Windows Update site so that if a Windows 8.1 system with these updates already installed, but .Net 3.5 not yet installed, goes out looking for the .Net 3.5 installation files, it provides a working set of files that will install the .Net 3.5 Feature.
Until then, good luck if you need to get the .Net 3.5 Feature installed on a Windows 8.1 system recently upgraded from Windows 8.0 through the Microsoft Store.
Regards,
The Outspoken Wookie