Recently, the Japanese Pokémon the Movie site ran a poll where users could vote for their favorite Pokémon. The results are in:
http://www.pokemon-movie.jp/election/

Greninja is first, Arceus is second, Mew is third.

Click 「もっと見る」 after #36 to see more results.

Yeah my man greninja got 1st! Suck on that Arceus (He normally wins)

Hmm, curious. Don't suppose they have a thing like this for any of the other regions, too?

I've considered making a thing where you could vote for your favorites, and it currently works with a few animals, but I don't know if it'd ever reach enough popularity to have a large enough sample size for high-confidence accuracy.

If you want to play with it, here it is: http://zorua.me/animals/

Heck, it'd probably be easy enough to make that to work with Pokémon. Getting the images is far faster for Pokémon than finding Creative Commons or public domain animal pictures.

*Goes over to zorua.me main page* this is completely unrelated to anything but you have a LOT of web projects o_o Also I'm totally not considering "borrowing" some of those duck photos for my signature or something.

Badger Photo? Yeah, that's the big one I've been working on lately. I got into wildlife photography last year, and my father will be contributing a lot of his old photos.

Looks like a gift is going to be distributed for our lovely #720 too

Thinking about it statistically, the poll only really had the Japanese voters naming their favorites. The top 100 (which is what they showed) is about as much as you can get a high confidence on with only information about favorites. I'm betting the bottom 200 or so were close enough that they were all only a few votes apart from one another.

However, I'm not surprised Simisear got last place. The elemental monkeys are fairly redundant.