I was thinking, that if done right and fans organize themselves they would be able to make a game that surpass the official ones of the franchise.
Now, I think it's not necessary to stick to the Pokemon trademarks (original Pokemon design, names and regions), but using Fakemon. Here in /vp/ Pokemon I've seen a lot of quality Fakemon to make a game with only these.
I guess there would be no problems at copying the game mechanics (I don't know how hissy are USA and Japan legislation about this, or if these mechanics are patented), but as long there are no problems, the game would go beyond being a fangame and be published, for example, in Steam.
*laughs* I don't really know...