The thing is, it's difficult to pick because we don't know what your story will be like. A story that heavily involves Legendaries, for instance, may be better off being set in Unova or Johto because their myths are well known and taken seriously, rather than Kanto where you don't hear about Legendaries that often.
The environments will also be very different in each region as well. Kanto and Johto are quite foresty and have a lot of plains, Hoenn is tropical, Sinnoh is cold and mountainous and Unova is urbanised. The types of Pokemon available also differ - if you want Water types, Hoenn might be a good place, while Poison and Bug types are common in Kanto. The starters also differ depending on region, so if you want a particular region's starters you might want to go with that. Think about gym leaders, professors and other characters as well, that might interest you or help with the plot.
Basically, what I'm saying is that in order to get the right region, think about your story ideas and pick a region that has a lot in common with those ideas in the games. If there isn't a region that fits your needs, or you want to make up your own locations and gym leaders, then a fan made region would be your best choice. I know that it doesn't really answer your question, but the thing is, a region is such a huge part of a fanfic (it's essentially your whole setting) that I think it should really be your choice rather than letting other people decide something so important for you, as it limits you to other people's decisions rather than what you feel is best.
