Also when Winuae crashes (great bit of software, but it does crash a little more often than Id like) youre left with a blank screen if youve replaced explorer with winuae. Any additional hardware manipulation needs to be done through windows, youre at the mercy of Windows viruses, system slowdowns over time, and so on.
If you havent disabled task manager via ctrl-alt-del then you can start explorer or WinUAE in a couple of seconds. Although it's just like any machine even an Amiga crashing just restart :-)
Viruii issues on Windows box is easy to manage, MS security essentials is fantastic. Although the chance you will get a virus on a Windows turned to Amiga box for gaming is very low as most viruii are via the web these days so if you are browsing inside WinUAE it becomes a moot issue.
Not too sure about the graphics modes, I'm very happy playing my games at 1440x900 full screen. The scaling is bang on, better than my old 80's Spring CRT monitor and actually fills the screen nicely. Workbench looks great too, now being able to use 1440x900 wallpaper :-)
OctaMed... tried it, can't find any flaws in it, even using protracker works well :-)
Almost at the point were I'll sell my Amiga collection TBH, I'm getting a better more enjoyable experience out of my WinUAE setup.