This has been mentioned hundreds of times before.
Having thought about it since it was first suggested, I think maybe a reason it will always remain like this is becuase it would significantly reduce the activity in a transfer market.
Upon obtaining the best trainees you could just build from within and with less need to upgrade using players that other managers had trained. Not just this but when the players did end up on the transfer list they would likely be unaffordable to most (because of insanely high skills and the fact that teams who use the transfer list to sell off their excess trainees to make profit would not have the money) Also, if you have 5 trainees that you can chose to train exactly how you like, why would you need to consider buying anyone else other than squaddies?
I'd prefer to train without limitation but its a part (massive part) of the game that we have all learnt to accept and despite its frustrations, I am happy that the BB's have stuck to the original set up.