It just gives me some control over them. I'll still let them happen. If 2 top 25 teams play each other and the lower team beats the higher ranked team then the result stands and if a middle to lower ranked top 25 team loses to someone outside the top 25 then that result stands. That way I still get upsets and there have been plenty of close calls.
There's no doubt that crazy upsets happen every so often but not to the extent that the game thinks they should. By doing what I do I may take some of the "fun" out of the game but I'll trade that for more realism anyday.
So far for the Heisman, I've seen QBs, WRs, and HBs early on. The HBs tend to fall off the radar for the reasons you stated but in the end it's QBs or the WRs those QBs are throwing to. In my 1st season it was pretty much Tebow, McCoy, and Bradford at the top of the list all year with Tebow winning it by 3 pts over McCoy.