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Gen V recently took the spot from Gen III for my favorite generation because of just how much stuff you can do in Pokemon Black 2. It just never seems to end. The amount of things you can do to occupy yourself is just staggering. Funfest missions, the medal rally, random Pokemon challenges, the Battle subway, Black Tower (Not sure of White 2's equivalent), the Pokemon World Tournament, the battle test, random online matchups, hidden grottos, Join Avenue, and just how long that postgame is to name a few things.
My biggest complaint is primarily about the region itself, despite that it's surface area is larger than in any previous Pokemon game. (Unova was larger than Kanto, and the additions in Black 2 are larger than Johto.). There seems to be a lot less variety in Unova than a region like Hoenn. Also while linearity was cut down quite a bit with B2/W2's Unova, it is still quite linear for my tastes.
