Look, I feel you on those points..
But, I think it is also important to remember that so much rotation is situational in real life (especially on defense). Using formation subs is a great way to get guys in. Also, for RBs, you could edit the stamina rating. I even have a little thing I will sometimes do with my RBs where I will drop their stamina a few points every time they go over 30 carries....simulating overuse....if they have games where they get a small number of carries, then I will bump their stamina back up (if previously dropped).
I know it isn't ideal....but Madden is all about the sacrifices you are willing to make. But there are lots of other little things you can do to compensate.