My suggestion is to place fines on teams that dont have players of their own nationality. The reason for this is because i see many teams with very few, if any, players of their own nationality. I think it would make the game seem even more competitive, especially for those facing teams of other nationality for trophys, and it could help for NT and U21 training as well. My thought is to allow X amount of players from different nationalities on a team. Then once you pass X amount of players that team has to pay a penalty to keep them. That way you could still have different nationality players for a big game, so they are borrowed, but then they could be sold to prevent paying the penalty.
Now by implementing a penelty you could do it as the player is bought on the market, or there could be another expense on the economy update showing so much money being taken out for the foreign players. This will keep lower divisions(4 and 5) from having lots of foreign players so they could focus on training american players for their own team. The higher divisions(3-1) has their own decision to have foreign players if they can afford the penelty.
I think by having a penelty it will force better training of a teams own nationality. This will help that nationality have better trained players thus making NT and U21 teams more competitive.
This is just a rough outline of what could be done and the outcomes of it but there are probably more ways to inforce it as well as more effects behind it.