The way I think me and my bro have decided to do this is the following.
The best Genin are all rounded up from all over the world and put into groups, which are then taught be the best Jounin around the world.
So, in a group of three there could be a Genin from the Hidden Leaf Village, a Genin from the Hidden Mist Village, and a Hidden Sand Village, and thy could all be taught be a Jounin from the Hidden Sound Village.
This way everyone is grouped up no matter what.
If you have any ideas that you think are better share them with us here leave your idea as a reply.