I view Unity3D with it's web viewer as more of a platform than a 3D engine.
Here's a link to an art project built with Unity3D (it may take a while to load - I used Firebug's Net tab to make sure elements were still loading) which I think shows Unity3D is much more than just a 3D game engine and definitely a challenge to flash:
http://www.everyday3d.com/works/installation/colors/
I have one client for which I built an interactive 3D visualization system. The project used Papervision and after trying numerous techniques to minimize the load it took on slower computers we ended up having to make it a 2D system because flash couldn't display everything we wanted to show effectively (it's also possible my Papervision skills aren't up to par and a Papervision expert could make the project work, I still have a feeling the visualization would still need to be limited). Molehill would probably really help this project out.
After building the above system, I started seeing more and more information about Unity3D. If I was to start the project again today, I'm pretty sure I would look heavily into using Unity3D over Flash for the visualization system.
The blog I mentioned in my first post has an excellent post about Unity3D's potential future:
http://www.everyday3d.com/blog/index.php/2010/03/08/unity3d-...