There is a way around it I think, well kind of. At the end of a Master League season it asks you if you want to 'store team data' or words to that effect. I am pretty sure if you say yes then you will be able to use the improved stats.
However, if this does work do not forget that the World Class players of today (The Nestas and Cannavaros) will have their decreased stats also. This is annoying, as I only want the improved young players.
To get round this I wait 'till people like Rooney,C. Ronaldo, Farfan etc hit their peaks in Master League, and then change their stats in the game to match. That way it's still fair because they're not stats that I have just improved myself "Rooney scored a hat-trick on his Man U debut so he must have 97 shot accuracy then etc." Some may see this as kind of cheating, but I don't as they're still stats that the game generates. Also I don't change classic player stats - they stay as default.
Has anyone noticed some of the players with super stats in the 'others' and 'unbelonging' sections? Stanley Matthews for instance, starts off with about 10 stats in the red, whereas default in-game stats are no way near this. People like Paolo Di Canio and Les Ferdinand have about 7 red stats also. It's just stupid