It depends on if your a Mac person using Emacs, or an Emacs person using Mac.
What I mean by that is that Aquamacs does things in a Mac way (e.g., storing preferences in Library/Preferences/Aquamacs Emacs/ instead of .emacs, and creating key bindings similar to other Mac apps).
I started using Emacs on Linux, and when I got a Mac, I first started with Aquamacs, but eventually switched just for consistency.
Just remembered something. Another thing that I didn't like (although it's customizable) is that instead of opening a new buffer in a window, Aquamacs' default was to open it in a new frame.
UPDATE: One thing that would be nice is to be able to drop a pre-existing color theme in and then tweak it with the color picker.