Im not sure what to point out to help in here, so I just let thinking flow.
In the real world are players people which have theirs moods,are unhappy with somebody, get sick, want to move and these things, so even top manager can be suprised by unfortunate events and sometimes doesnt achieve what he planned...
Here if some teams catch the train soon and know how to survive, is hardly possible to get them. I think that changes like better merchandise revenue if you have raised drafted players, is the step into right direction, because you can prepare your team into condition which will be more efficient, however is truth that once you want to move from 2DIV, your team have to demonstrate great ability, which possibly cannot be made meanwhile you train 3 of your 21y centers-drafts on PG position a passing skill...