* What is the level of Amiga OS3.1 support?
Quite perfect.
Softwares like IBrowse, Directory Opus 4, AmiTradeCenter, Wordworth, Photogenics, TVPaint, Wipeout, etc. just work fine (and much faster than on a real 060/CGFX Amiga).
* Can it run WHDLoad style games? (be gentle with me here!)
Not directly, but e-uae works fine with it.
* What is the Native application support like? (Office type, Web browser etc...)
Showgirl (advanced picture viewer), Sputnik (browser), AmIRC (native version), AmiNetRadio (partially native), etc. lot of native application for most operations.
I don't know about AmigaOS 4, but MorphOS is just a great AmigaOS you can use for every day computing.