I absolutely agree with you. I think you should be able to have complete control over the training of your players. If you want to train your C in outside defense you should be able to do so (and thereby make a mistake).
Of course certain skills should be very difficult to acquire for certain type of players (i.e: a C in outside defense), but if a manager still wants to do that well that should be his problem and his right...
This would be the key to implementation.
So let's say that there was a training factor associated with each training type and skill and position. For example for "pressure training", outside defense might be PG 1.0; SG 1.0; SF 0.8; PF 0.6; C 0.5, and the inside defense component might have factors of PG 0.5; SG 0.5; SF 0.7; PF 0.9; C 1.0..
So if you chose pressure and PG, your PGs would get mostly OD and a little bit of ID. If you chose pressure and C. your center would get mostly ID and a little bit of OD. So if you wanted your C to get some OD, then you could train pressure and C; but it would be more efficient for you to play him at PG and train pressure and PG.
If you chose pressure and PG/C, then the training would be cut in half, but the concentration for the positions would be more appropriate for their positions.
This would still work even if the ID component for pressure is less than the OD component.