The CPU's cone affects gameplay in a pretty major way b/c w/o it, the DBs don't 'read' where the QB is going with the ball before it's thrown as often, so it leads to less user picks and a better QB QB passing %...tougher to defend the pass, etc...
The sub in / out thing is a little nitpicky, but that's a realistic setting and since my D rotates out at the end of 10 play drives and leaves me with subs in the redzone at times, then the CPU should have to deal with it as well...
I also like to see them have to sub in a second HB on occasion...