For me, Launcher Pro has three advantages:
(1) the ever-present icons in the dock at the bottom of the home screen (which you mentioned). No matter what home screen I'm on, I can access my phone, my contacts, or my note taking app without having to flip a screen.
(2) More than 3 home screens. I'm using 5 now, but keep them all clean (only 5 or 6 icons) so that my wall paper shows through. My main "home" has CalWidget, battery percentage, etc. One that has "travel" things on it (Google Map, speed dial calls, flashlight, My Tracks, etc), one that has "internet" things on it (Newsroom, browser, messaging, etc.), one that has time killers (games, books, etc.) and one that has misc. apps I use all the time. Getting ready to switch to the Droid X next week, so by default I will have the 5 (or 7, can't remember) home screens.
(3) The ability to have 5 rows of icons, and icons without labels (I know what all the icons stand for, why clutter the screen with labels?).
Granted, these are all cosmetic things, but for me it helps me keep my Droid less cluttered looking and more organized.