I feel that the most imposing, brooding, and lissome of villainy is that which one does not see - what is feared most - flaunting on the indulgence of the understanding of others. When the depth of intent is indiscernible and when the villain's incentive can never be figured out so as to not dampen the impact of the villain, I feel a certain intangible, complicated, but fearful complex bears to fruition. Pokémon has nothing of the like, of course. I feel that it's not dark or deep enough to quite reach the threshold of that level, but while the villains may be apocryphal, at least they're not simplistic. Jessie, James, and Meowth are both human and criminals. They're in shades of gray rather than simply black and lambently white. It sullies and belies the trio, which doesn't by necessity add to their complexity but their depth; what one can relate to. But black and white is usually what "good and evil" conflicts ring of for me - there's villainy abounded in Pokémon as it is with the kind of challenges the characters face - themselves, their Pokémon, their rivals (who are, by nature, hostile), and what not. Villainy does not have to be in the form of antagonists who take expected form. I prefer hidden and deeper threats myself, and I sort of like that Pokémon breaks away from the refrain that is "good versus evil" on select occasions. And most of the time that just leads to inane clashes that get nowhere anyway. Still, I feel villains are people who need to challenge the heroes on a mental level more than a physical level, something a tad lacking in today's media in general. In the eyes of an enemy a hero must become more than something that just surmounts to an entity. Great heroes merit great opponents.
The series does bring to fruition the occasional thugs, Team Rocket, Team Magma, Team Aqua, and some other villains, but because of the somewhat lighthearted and less in earnest nature of the anime (and how it tends to stay an RPG format more now, like the games, being battle centric), going any deeper than that may be too serious for the writers. As far as movies go, some of them suffer from a lack of thoroughly developed villainy (Mewtwo) and some of them suffer from a lack of finality and a good swell in tone (Rayquaza), whilst others are quite morose and inscrutable by nature (Unown). The only thing I think could get old fast in Pokémon is having an anti hero who occasionally takes upon the role of a villain. A vigilante, even. I just see them as excuses to garner attention, whine, and lose themselves in their own searches. But as of now I'm okay with the villains... I sort of wish that the comedic relief role wasn't so pensively kept to but with an anime like Pokémon it's to be expected.