Very nice topic Lemon!
My priority would be to attract more people training skills, rather than just satisfying further those who already train but the number of trainees wouldn't increase much.
So, one option would be to be able to train both skills and GS.
If that can't happen, firstly i would set a very specific weekly minute range, within which a skill trained player would see his GS/DMI behave as if he was trained in GS.
It is unacceptable what is happening so far.
This way those who train but are frustrated with the current disadvantage(and give up) will happily keep on training, while at the same time, those who train GS but manage their minutes, will have a motive to start skill training.
Then, i would guarranty that when "strictly follow depth chart", "let them play" and player set as starter/backup/reserve, are all applied, then the player, no matter what, plays 48 minutes (unless he's injured of course).
I know(we all pretty much do) users who paid for a Utopia team, just so they can train three (usually home)players and couldn't do just that. Without worries about league position, promotion/demotion etc.
All they wanted was to train three youngsters and they couldn't. Others quit their team, others stuck to one trainee, others just abandoned training all together.
Lastly, in that first packet of measures, i would do something about the number of existing trainers, their salaries and of course the fact that their salary increases every week.
It's all a travesty as it stands. Simple as that.