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Even though I like the last 2 gens as well, Gen III will always hold a special place in my heart because it's the very first generation I played Pokémon in.
I have to say that I loved a bit of every generation - the Pokemon of I and II, the map/region of III, the Pokemon of IV, and the story and characters of V. However, if I really had to choose, it'd be a tie between Generation II and V for just being the two that always pop up first when I think 'Pokemon.'
I actually have a confession to make. I've never played a 3rd Gen game. Yeah. I know right. Know what, I'm gonna go buy one off E-Bay. Now. For my crimes.
But which to get....?
Like many here, I like a little something from every generation. Gen I has probably the best pokémon imo. Gen II has the best region. Gen III has the best gameplay (yes, I prefer the old style). Gen IV is generally cool and brought back Johto, so! Gen V is, almost together with gen II, the region with the second best repertoire of pokémon imo. And the main story in Gen V is more interesting than the others.
But the ones that come out on top are actually gen II and V. Gen II for having a little great stuff of everything, the first day and night system and weekly events among other things, while still keeping the old school gameboy style - and of course it has Johto! Gen V is superior in many ways and I can't be bothered to mention them more than I've already done, haha.