I completely disagree with your opinion, Nicolas.
I was always annoyed that the popups were available in mobile version of Wiki but not in desktop version. When I looked at the Beta-Features for the first time now I was very happy that it exists and instantly activated it.
Although I'd consider myself a "Wiki power reader" I realize now that I was never a power user since I never heard of "Nav.popups" nor of Wiki-Skins at all.
So I forcefully question that 99% and assume that you are in a type-of-user bubble were you might feel that way.
In addition we must not forget that beta features are intended to become standard one day and in that stage they will reach a lot more people than any skin features ever will.
And this is one feature I think will make "wikiing" much more comfortable even to those users that aren't aware that they are missing out this comfort at the moment. So did I: as mentioned above as soon as I got used to that feature in mobile version of Wiki I strongely missed it in desktop version.
Just not enough to google it, I suppose, since I just didn't think there was any possibility to adjust Wiki's look and feel at all.
So on the whole I suggest you just consider this beta feature to be the navigation popups feature on it's way to getting a standard feature. Which it truly deserves, I think.