Those are some good points. I hope some of this stuff will get fixed.
The depth chart thing drives me nuts. I often end up carrying 6 active CBs on my roster, and when I do mass subs I want to see that 6th CB be used in dime, or at least a 5th safety. Instead, invariably it puts my #3 WR, a backup RB, or even a QB in there. So basically I am forced to run nickel at most after doing mass subs, and if one of my CBs gets tired I have to call a timeout, or put the first string back in, or stick to 2-CB defenses. So lame.
As far as the CPU not subbing... It's one thing that when you play vs the CPU there is not very good subbing. What's worse is that when games are simmed the teams still don't use their subs. Only your top 3, maybe 4 CBs will record any stats.