The Options button is a key one. The thing is tiny and aggravating to push. For any game that you end up using it a lot (ie, Dragon Age Inquisition) it gets annoying really fast.
Other than that though I have no major complaints. The touchpad I don't see as useful but it also doesn't really get in the way either. Bigger battery - yeah it would be nice but its not hard to keep it charged up (I just keep a second cell phone charger near my nightstand and connect the controller when I'm finished playing).
If they just got that options button taken care of that would work great.
Also - a cheaper wired version would be nice (even if third party). My 6 year old likes to occasionally play Skylander Co-op, but she generally doesn't need a great controller (and keeping two charged up is more aggravating). The availability of a ~$15 second controller is why we're still playing that on the PS3 instead of the PS4.