It depends. Let's put all plot/character/etc. issues aside. Let's talk about pure looks. For some Pokemon, they look better in the anime. Others have better in-game sprites. I personally think that Leafeon's sprite is adorable. On the other hand, I'm not fond of its looks in the anime. Then there's Scizor. It looks awesome in the anime and the recent sprites, but its bright orange-ish ones from the 3rd Generation are a bit frightening. Then again, I dislike most 3rd Gen sprites, so I'm really biased.
However, I love the anime's ability to make the monsters seem real and it's also fun to see their attacks, which I like. They also give a personality to most Pokemon, which is also nice.
But, of course, the games are more fun in general.
Let's talk attacks again. It's great seeing what the attacks look like in the anime. But a lot of it isn't logical. (AIM FOR THE HORN! THUNDER ARMOR! EVERY ATTACK SPARKLES IN A POKEMON CONTEST! MY THUNDERBOLT BREAKS YOUR SPRINKLERS AND PWNS YOUR ROCK POKEMON!) You get my point.
I'd have to say... Sugimori art wins?