I'm a bit short of time now to quote and edit your post. I think the ideas of training different players in different skills each week is great for a single player type management game (like FM for example). I think that in an online game with users coming and going, though, the problem is that if everyone can train optimally and compete optimally every week, as most "full team" training proposals would have, this would simply make it easier for teams at higher levels who generally choose to sacrifice training because of the competition at the top.
I think there needs to be a clear and meaningful choice to be made in terms of training and competitiveness - the current method of making them play in a position for 48 minutes is one way of doing that. I'm not convinced it's the best - I'd rather see sliders where you can put a percentage of training time into stamina, a percentage into FT, a percentage into GS and a percentage into skill improvement, and then just training the players who start in the training position so minute maximization is no longer required.