Well,
I like the youth team idea because it adds something different/extra and a new way to manage your team.
Why not just limit the total number of new rookies a team can get to 3 or 4. which means that even before the draft, or after the draft but in an extra in between phase the manager sees all the rookies, the draftees and the youth team rookies, that he can promote and has to choose 3 or 4 of them. Before having the final skills/potential etc revealed. Depending on how much info we give away it might not matter as much because the total rookie number will stay the same and we still don't know everything.
just an idea