I can see why you might want to share some libraries between a phone and desktop app but running the same app on both platforms makes no sense at all to me.
Then you have the problem that universal apps have to be sold through the app store which has all the problems of the Mac app store except worse in every respect.
From my point of view, I find your statement bizarre.
Universal Apps : Native :: Responsive Design : Web
Creating separate applications for mobile and desktop is analogous to the old-fashioned approach of creating a web site for desktop consumers and an entirely separate site for mobile users. Thankfully, with the advent of what we now call "responsive design" (which is admittedly poorly named; should have been "adaptive"), we no longer need to create two separate apps, but instead can tune the singular application's user interface to adapt to screen size.
Universal Apps work the same way, they adapt to screen size. And with the nearly continuous spectrum of screen sizes from phones to phablets to small tablets to large tablets to small desktop displays to large desktop displays, there's a great upside to using such an approach.
Have you seen how the new Outlook app adapts to the a full-size display using Continuum? It's pretty awesome.
Frankly, I'm not really sure why you wouldn't use that approach.
That said, I agree the app store model needs to be reconsidered by everyone.
Then you have the problem that universal apps have to be sold through the app store which has all the problems of the Mac app store except worse in every respect.