I could see this working if they placed roster caps on both the parent and farm clubs.
It might also provide another avenue for teams to make up ground on the top teams and to experience other aspects of the game. If you are a middling top division team you have to try and maintain a certain quality of team just to stay there. This makes it difficult to play draft picks or very young recruits.
Having a farm team provides the chance to develop players and use them, rather than just try to train a guy for enough pops enough to make a profit and spend it on a player you actually want.
Either way is fine with me, but this could potentially add a nice dimension to the game. It may provide the opportunity to add a supporter feature or two as well.