Browser based free to play MMORPG Pokemon Online Game PokemonCraft Developer
PokemonCraft has more than 250.000 registered members around the world and you should check it's Pokedex
...I would wager it was because it was a fan game capitalizing on Nintendo's IP. ._.; Or even if it wasn't making any sort of profit, using copyrighted material is still illegal and that is what any fan-game faces. If Nintendo sees it as a threat (ie, it's getting too popular, or people think it's official), they have every right to close it down.
:/ But this isn't really relevant to PC so I'm gonna lock it.