I'm disappointed in the mere existence of the hardware buttons. Having them as software on the Nexus meant that I could download a ROM to change their order and/or add new ones. There's no way I could go back after having that sort of customization available to me.
(True, it was a bit of a failure that such options were not available by default, but at least it was even possible.)
Other than that, I honestly can't see what's so supposedly bad about the design (particularly from those who seem to focus on the pebble blue version to exclusion.. you realize there's a white option, right?) but maybe I'm just too technically inclined.. I value those little conveniences like removable sd card and battery too much.