Emerald, I've played it countless times and I still have tons of fun doing so. Platinum is my second favourite. Also FR and LG because I loved the original Kanto and was great to go through it and the new Sevii Isles on the GBA.
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Pokemon Platinum, Heartgold, and Soulsilver are the best games imo becuase there is alot of stuff to do in them after beating the elite 4 and champion.