> It takes over the primary desktop which results in very weird behavior with the Dock.
Not sure what you mean. It's pre-Lion style full-screen, not weird at all. It just hides the menu and the dock.
I'm not sure I agree that Emacs's GUI support is "token" but I would admit to it not being the emphasis of the program. I give them a lot of credit for having a Mac port in the main codebase and keeping 3 or 4 disparate GUIs in sync with each other.
Scrolling with the trackpad is crazy fast by default, I had to slow it down with the "mouse-wheel-scroll-amount" customization (I only did this after multiple years because it doesn't matter that much in the end--I realized that if I'm using the mouse in Emacs I'm generally doing something wrong).
Smooth scrolling is anathema to Emacs which doesn't even let you resize the window in sub font-height increments. I don't think that decision is necessarily correct but I think it probably comes from Emacs's heritage as a terminal program. I think smooth scrolling could be nice. I do have to say that in the long run C-v, M-v, and C-s end up being way faster and more accurate than 2 finger scrolling.
A funny aside, I did one of the first (if not the first) port of Emacs to OS X back in the Mac OS X Beta days and someone sent me an email saying the menubar was blank--there were no menus in the program. The funny part was I had released it and had been using it as my main text editor for weeks and I never even noticed. :-)