I dunno about which specific Pokemon he'd hate the most, but he'd LOVE the games.
Pokemon takes his ideas, his Theory of Evolution, and makes it completely accessible to everyone, especially the young. Sure, it takes a lot of liberties on how "evolution" works, but those liberties makes his theories fun for everyone.
I doubt he'd be an avid fan, but if he were alive today I'm certain Mr. Darwin would own at least a couple copies of various Pokemon games and play them now and then.
http://www.youtube.com/watch?v=gJN-SWGei7w <- Eyegasm: Xrd Official KH3 Aerith, apparently? How...?
Relicanth, due to it's failure to evolve despite the length of time it has existed.
But it's only survived because it's lived in a very closed-off, limited environment with no apparent predators- it has no need to evolve.
Well, presuming we're talking Darwin being taken from reality and transplanted into the Pokemon world (His theory wouldn't have been what it was if he was born and raised there), the living inanimate objects would be the biggest head-scracther, no question; they have no predators nor seem to be prey for anything else, we don't know how most of them reproduce, or more importantly still, how they became animated at all.