My dissapointments with the anime are...well...many ^_^' But I guess I can sum it up under two things: making pokemon behave too humanlike/doing stupid things with them such as making geodude float, and all the wasted potential plot-wise. No offense to anime fans - heck, I watch the thing myself from time to time, just because it's Pokémon.
In terms of pokemon: I like thinking of them as slightly more intelligent animals (with some notable exceptions, such as Legendaries) who are trained by command, and I write my fanfics/pokemon behavior theories based on such a view; then I get all the anime fanboys on me whining "oh noes all pokemon are sentient you're wrong!/they all magically understand human languages/they all have the ability to talk look at Meowth!" Ugh. I like realism in my fantasy, and the crazy lengths to which the pokemon are humanized just destroys it all, to me. And from there comes the ever annoying question of what's in the burgers because oh, people wouldn't dare eat such noble sentient reasoning creatures >.> I won't even comment on how silly floting geodudes look, or electric attacks hitting ground types.
As for the wasted potential, it's too much to mention. They could have done great things with the anime (they could have made it more like Pokémon Special, for one), but they choose instead a formula plot for most every episode, throw aside story arcs (GS Ball and Team Aqua/Magma especially), stuff it with filler, and generally repeat it all for almost 500 episodes >.>
Man, I'm not easy to please am I? ^_^;
