I've played every generation except for 6, and I'm partial to Platinum, for some reason.
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My favourite game is the one I first played (big surprise)- Pokemon Emerald. I know a lot of people dislike gen 3, for good reasons, but the drawbacks don't really outweigh the benefits to me. The story was great, the pokemon designs were great and the region was great. In comparison to a region like Kanto there's a lot of variation in the environments you see in Hoenn (though there really is a little too much water, though I don't think it's as bad as some people think). The remakes in generation 6 were also great, and take a close second place for me, for fixing all of the problems from the gen 3 games and adding a load of new content.0