Application switching, I can't figure how to get from mail to contacts or to calendar without going to the home screen. Annoying.
Ditto the OP's issue with in and out of holster awareness / behaviors.
HTC, take it from the BB world, the bright multi-color LED notifications work. Next time dont hide the LED.
Physical button for the camera. It was great to be able to pull out the phone and start the camera function before I was even looking at it.
OK I'll say it, battery.
My email issues:
One-touch filtering of a sender in the in-box, I used that all the time. On the Storm 1 you just touched the sender in the inbox list view and held for a second. You got the list of everything in the folder from them.
The ability to select what Outlook folders showed up in your inbox.
Contact-based custom email notification. Really miss that. Now I don't know when my wife emails me. I only can have one account (my work exchange acct) vibrate so I know when those hit. I used to be able to have different vibrate patterns for verizon mail and work and my wife.
All that said, I don't want to go back.
Don't get me wrong, I love the speed and power of this baby, and I know many of my issues are either a getting used to it thing, or a missing app thing.