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I personally really liked the sprites and some areas I think couldn't be topped even with top tier 3D graphics. But my main problem with the 3DS games so far has been that the games as a whole just aren't that good, and I don't mind 3D models if GF would put more effort in them.
I am kind of sad though that even PMD went 3D, I really would've liked at least one spin-off game that still kept sprites because I think sprites and Pokemon just kind of fit together.