I totally see your point, that was one of the criticisms I had thought about already. I can try to rebut in various ways: a manager who decides to follow the course I proposed first of all would need to spend more in Scouting Points, this is already thought in order to avoid people abandoning their leagues completely. Furthermore, we already have a difference in drafts: a team in one league can spend more than a team in another league for Scouting Points, but the team who spent less will get a better draftee because of, simply, good luck.
However, my proposal is not flawless: the Rookie Market is bigger and there are more chances. But it seems such a waste of talent to have so many draftees that will be lost just because they will never enter the market in any way. I think my proposal is not hurting the game dynamics, actually it would improve the average quality of draftees that are actually playing in the game.
Another solution might be possible: in the Rookie Market, a team could be allowed to only buy one draftee, avoiding stashing good rookies. Or teams buying a draftee on the Rookie Market would then have to renounce to the highest-salary draftee they obtained through their own league draft.
How does this sound?