Having used OmniGraffle since version 2, I'm really impressed by the new improvements and features. As I'm mostly on a PowerBook with a widescreen display, I would prefer the seperate toolbar in a vertical style similar to Photoshop. Having the toolbar outside the document on the upper screen border, it needs too much space, especially, if you have paper layout (more high than wide).
As others have mentioned, the Icon is really ugly. I still use the one from 2.0. It's not perfect but it doesn't burn your eyes.
The text-button (labeled with a A) in the text palette doesn't look like a button that reveals the standard OS X font window. I'm not sure what's wrong with it, but I don't like the look.

Otherwise OG looks and feels great and it's usefulness for my work has been much improved. I'm looking forward to the final version with a new manual (to find all the new features) and hopefully some new stencils (the one that are shown on your beta-website).
Highly recommendable.