Cursor keys on the on-screen keyboard!!! (touchpad)
WebOS phones should have a slide-to-answer gadget, not accept/reject buttons when a call comes in and the phone is locked. My Pre 3 has done random things when a call comes in and the phone is in my pocket. Sometimes it picks up, sometimes it rejects, it depends on which button thinks it was pressed in my pocket first.
A dedicated task-manager.
For the Pre3, a voice dialer that doesn't crash the whole audio subsystem.
Music apps should be able to exclude or hide certain folders of your choice so as to hide non-music sounds from the player.
The music app should have had built-in equalizer controls since a hardware equalizer apparently exists on both the Touchpad and the Pre3.
I should be able to drag and drop photos from one folder to another in the photo app. I should be able to select multiple photos and copy/move/delete them without having to do so one at a time.
The browser should be able to keep in memory at least one page in history as opposed to having to reload/redraw it every time, especially on the touchpad. I can understand if memory is low, but if you have no other apps loaded and only one uncomplicated web page, it shouldn't have to reload a page when you go back.
A much better VPN client that allows for an RSA SecurID. The current VPN client makes it very difficult to use one.