Cup league can be fixed if they take the average quality during the season instead of the quality at the end of the season. A lot of teams sell all their good players to get a low quality rating and then buy a whole new team at the start of the new season. There is no logic in that approach. I will state it again Cup punishes the good players that keep their team intact.
About the youth acadamy, it is just a source of income. That is it. Treat it like that and not as a place where you can spend tokens. I would spend tokens on the acadamy if there was a chance to get a 5 star youth with a SA. I would gladly pay 12 tokens for that but not more.