I don't really see a problem with the 3D map. It's more a thing I dislike a bit and something I would prefer to have replaced with an old, worn map. Something that you can actually believe that you hold in your hands.
I'm not really sure about anybody else, but for me personally, that would feel more "RPG'ish" and thus more fitting than something similar to google maps...
Why should it be a worn or old map? Skyrim is an active province. Doubtlessly people would constantly be making new maps to sell. TES may be a fantasy setting but I see the word "medieval" pop up lots. The world of TES, if I recall, is older than our own civilizations in the real world. Magic may have made technological advancement unnecessary but that doesn't mean everything should be old, worn, and rickety in my opinion. That town with the wind mill is a good example (backwards sail debate aside). It's a flourishing town with operational commerce. A town like that wouldn't be producing old and worn maps. Maps get old or worn with time. They don't start out that way.
This reminds me of all those stone Greek statues from ancient Greece. I took a class about Greek mythology (required cultural class) and it had a section where we learned about that ancient art. As it turns out, those statues were actually like three dimensional paintings when new! They were in color, and looked very different from how they look now or how most people imagine them! The professor said that the actual artists would probably be aghast to see their creations displayed naked without the paint that was washed away over the millennia. Yet when you see new games or movies about ancient Greece they show those statues as plain stone statues... not at all how they looked back then. I liken a worn map like that. We have these old maps from medieval times, but that isn't how they were back then when in use just as those Greek statues used to be beautifully painted.
http://io9.com/5616498/ultraviolet-light-reveals-how-ancient-greek-statues-really-looked
I understand it's just a preference of course, and there doesn't have to be a logical explanation for it. Personally I welcome the 3D map. I'm disappointed we can't make custom notes, but I hope we can drop markers of some sort. Either way, I'm very much looking forward to seeing this map in action!