Alright, so I was thinking...
since the countries are getting renamed to the villages (Rice Field->Otogakure, etc), Konoha will have no place to go since Fire Country will become Konohagakure. So, why not add 2 villages (since their are so many unique shops in Konoha) and divide all the shops up between these 6 villages. The 2 new villages would be Iwagakure and Kumogakure (Hidden Rock Village and Hidden Cloud Village), since they are the remaining "Five Great Shinobi Countries" that are not in the game yet. With these villages, there could also be other custom shops and have their own races, etc...
This is just an idea to solve the problem that will inevitably occur once the countries are renamed. Comments? Ideas?
Edit: I just remembered that Iwagakure is in the game...as the Hidden Rock Village. So...maybe convert the Hidden Rock Village into Kusagakure or Amegakure (they are lesser shinobi villages) and add Iwagakure as a new village.