The 3DS version is more streamlined and visually pleasing, I think, and there are just so many small improvements that I think it makes for a more enjoyable playing experience overall. For the most part, the changes they made are positive, but I agree that there are some things that seem... ehhh.
That darn Shiekah Stone that's bouncing all over the place near the HMS, for instance, breaks the mood of the area for me. The bar doesn't look as good as the clock, and the boss eye is actually kind of insulting (it makes me think the developers got together and said "gamers are too dumb and clumsy to figure out and kill these bosses as they are, so let's give them all giant shining eyes for weak points"). Outside of these few (and minor) complaints, I think the 3DS version is a big improvement.