The Good:
Porygon2. They did a great job with it's sprite, and it looks so darn cute!
Suicune looks brilliant.
Ho-oh is magnificent, and though it's head is a bit small when compared to the proportions of some other Pokemon, that's more of the other poke's problem.
Pikachu looks nice compared to the weird DPP sprite...
The Somewhat Awkward:
Gallade resembles an actual pokémon trainer rather then a pokémon. I could just imagine him replacing Gold...
A similar case with Gardevoir, along with the fact that it looks like that she seems awfully thin, as if a single punch could smash her...
Mr. Mime...Urg, lets not even go there.
Machamp was never able to pull off the Chibi-thing well, as shown in PokéRanch. This only strengthens the statement.
Krabby never faces the direction you want it too...
Run, don't walk, from Chikorita...
Porygon-Z's head is bigger then it's whole body put together.
Pygmy Tyranitar anyone?