net, I think there is some credence to what you're saying, although in HD, it's pretty easy to really improve a small conference sim simply by getting human recruits and some decent coaching in there, often against weak competition. So the significance of the "turning the program around" aspect pales in comparison to real life.
And while I also agree that it's silly that so many schools appear as a step backwards, what you simply need to do is ignore that, and evaluate if you think the move will be a clearly better situation long-term. If you're at Dartmouth, and the sim is saying step backwards for Pitt because they've been down recently, I'd still say that is a clear step up for you. Follow your common sense, not the step backwards advice, and you'll be fine.