Number two is my biggest peeve as well. The problem is that the CPU seems to be programmed to throw to the open receiver and not necessarily to the best matchups. The autosub settings help this a wee bit, but not enough.
The other issue is that the CPU doesn't perceive a guy as being open when he has a step or two on the db. This causes issues in which you can't tighten coverage to realistic levels without the QB going into checkdown mode.