The best anime ever? That's kinda subjective, isn't it?
Well, between these two (again), I'd have to say that Digimon has the better Anime. Why?
For starters, Pokemon rather rigidly follows the games, while Digimon has more freedom. Thus, while the anime has been stagnating for years now, at least Digimon has fresh story lines every season.
Also, Digimon tends to be a bit darker than Pokemon at times. (For example, season 3. Good God was the latter half of that anime disturbing!)
Not that I don't like either, mind you. Picking this topic is kinda obvious, but with so many animes to chose from, maybe simple is better...