Some Pokémon did very well in the 3D transition- Wigglytuff, Archeops, Aggron, Gengar, Mr. Mime, Magikarp, Accelgor, Spinda, and Ludicolo, to name a few.
Others didn't do so well.
>Salamence
>Xatu
>Swellow
>Haxorus
>Torkoal
>Hippodowns
>Hitmontop
>Vileplume, a little bit ; - ;
>Parasect, to a degree ; - ;
>Flareon
>Kabutops
>to name a few others.
Overall, I sort of miss the 2D sprites sometimes- a lot of my bros, such as the aforementioned Vileplume and Parasect, really lost the 3D model lottery, and many Pokémon just had way cooler sprites than models- but overall I'm not adamant towards the shift.
The future is now, thanks to 3D modelling!