In the first season the zombies were able to turn doorknobs and pick up stuffed animals. How or why did that change?

I think it was because it was too un zombie-like. I mean most people think of zombies as mindless beasts that eat people. Not undead beings that can open doors and pick things up.

After the CDC episode we learned that only the brain stem worked which would make sense that they wouldn't be able to do things like turn doorknobs, etc...

Because as time goes by, the walkers keep on rotting. So the more a body is rotten, the more it's unable to do stuff. That's why now they're slower, they're easier to kill, they get stuck everywhere, they're weaker, etc. It's biological.