I think you can't just get a free for all system (or some variant of it). So complexity must be retained.
I agree that players develop through playing time in the NBA and even in Europe. They set the threshold at 48/week but whatever the number I agree with Trainerman that there is correlation between burn and development. I'm fine to retain that aspect of the system to some extent as long as we get more flexibility.
To be fair I'm on board with any proposal to add flexibility to the current system and hopefully that's still considered. I still train my guys out of position (and my main trainee is 24 and the best player on the team), but if I could somehow, even under equally strict conditions train a guy in pressure and another in outside shooting I would be already a lot happier and I think it would be easier to understand and accept as a system by many new managers.
Just a quick idea, since we're in suggestions, and I'm not going to bother to put too much thought into it because I doubt any of it is likely.
New training: Each week you have 144 (3x48) minutes to spread out among any of your players. Each player can be given a specific training type to focus on, regardless of position played. However, they can only be given a number of minutes equal to the total of league minutes plus cup minutes plus half of scrimmage minutes, with the max of 48.
Each team will set the percentage of their training for:
Stamina (5% min / 25% max) -- for all players
FT (5% min / 25% max) -- for all players
Game Shape (5 % min / 75% max) -- for all players, though the minutes they play is still the base component
Skills Training (5% min / 75% max) -- based on minutes/regimens selected
I think the percentages are way off but as I said, not going to put much more thought into something that I doubt will ever happen. But this way you retain the minute-based requirement for training, make playing guys in competitive games mean more than throwaway games, eliminate any position-based problem to it, and still have to make meaningful choices to balance training and game day performance, plus eliminate the 0.00 FT percentage shooters without having to have crosstraining implemented.