Limitations change as API priorities shift. The platform has grown over time. Some inherent limitations are useful (to be a medium to creativity, to the user's control over their system overriding a developer's narcissism, to the idea that security and reliability are worth engineering for), and yes, unlikely to disappear entirely.

I can't dispute the unpopularity of Windows Phone, but from what I hear the Windows Store is fairly successful in Windows 10. Many consumers use it to install apps, which is a judge of popularity. However, if by popularity you instead mean sentiment, then I get the impression that currently most people are ambivalent about the Store in so far as it is a pragmatic tool that people neither love nor hate, just as most people neither love nor hate their toaster so long as it toasts. (Certainly there are haters, but volume of their voices is not necessarily an indication of their size/number/consumer spending activity per the first definition of a popularity, just a reminder of the passion with which they feel their sentiment.)