Hehe.. i actually did a lot of thinking about this (too much free time) both "settings" have lots of potential and are interesting in their own ways.. but IMHO only if you ignore everything the game/movies shows you. Why?
Because they are dumb. The way they shows things just doesnt make sense.
ex; in Harry potter i think that mages are basically walking a very, VERY thin line between statu-quo and complete chaos because they are so patheticaly ignorant of everything muggle-related (and eventually their magic wont protect them against the ever-improving muggle technology and communication systems). They are a very few millions hiding (themselves and countless magic creatures, plus magic-owned terrain) in plain sight of billions in a world wich is going foward without them.
And in pokemon, well, its an idealized game world meant for kids. So it doesnt make any sense at all. Its too clean, nice, full of holes and cliches. If "realistic" in any way, pokemon would be pretty hardcore as a setting. Its why i like thinking about it; just what happens if its "realistic". Its basically a survival game on a planetary scale, and humans arent winning if they are acting stupid or careless in any way. Oh, and your average PK is perfectly capable of killing a human on a whim, but they are sentient just as humans are (just look at the animes).. few are dumb, even if they behave like animals.
So wich would i choose? HP, if said Harry isnt anywhere near. Pkmn if its realistic.