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World of Warcraft now has a fully featured Pokémon clone game built into it. Some/many of you may already know this, but I had no idea that "pet battles" in WoW were such a robust game-within-a-game. So for others out there who have been wanting to play a Pokémon MMO that isn't a fan-made emulation, I recommend checking out WoW, which you can get at the moment on sale 75% off direct from Blizzard.
There are almost 1000 different pets, and they come in different rarity and breeds (which affects stats). Each pet has 6 abilities (you choose 3 to use at a time) and battles are 3 pets VS 3 pets. There is pet hunting in the wild, pet battles VS masters and grand masters NPC (think "gym leaders" in pokemon), including some legendary tournaments. Also there is a matchmaking system for battles VS other players, or you can challenge anyone directly.
The sheer number of pets and ways to get them is even beyond pokemon-level and could easily keep you busy for years. The only downsides I've found so far is that I kinda prefer a bit larger team size (maybe 4-6 per team) and so far they have not added rankings for players. But I can overlook both of these issues, since this is definitely the best legit Pokémon style MMO available, until Nintendo makes their own (which they never will).
If you have some questions feel free to post and I'll try to answer.