1) My Amiga doesn't _need_ any settings to be tweaked. It just runs fine all the time, whether it be graphics or games or whatever.
2) How many times have you been using a real Amiga when all of a sudden the screen goes black and some horribly friendly dialogue box for a completely different app comes up?
3) UAE is a pig to set up for full-screen displays of the right size and right aspect ratios. I like to be able to switch between 1280x1024x32 to AGA PAL 320x256 and still have everything look right _without_ twiddling settings.
4) I like playing around with odd hardware. Can't fit a Zorro III card in a Windows box.
Considering that it is more or less impossible to work around some of the issues above when talking about emulation under Windows. Some issues are so obvious that one simply has to accept them or just decide not to use the emulator just because one can't handle the obvious consequences.
I have yet to see WinUAE run as smoothly as my Amiga on any system (and I've seen some quite good systems). I know my Amiga was way more expensive (Cyberstorm PPC, 68060@50/604e@200, Voodoo III) but that's not the argument. WinUAE is good - but it's not thatgood.
I do see your point, but it's not like there isn't issues with real AMiGA:s either. I've tried to come up with a good solution on switching between RTG/AGA in a smooth way on my A1200. Bought myself a flickerfixer/scandoubler and thought that was nice... until I realised I had to get a monitorswitch aswell, and then suddenly the quality of the signal will be somewhat less unless some big money is spent. And even after a monitorswitch is bought, there will be some delays when switching the screens and the AGA frequencies are still rather low so that some monitors don't support them and so on, and so on. I've yet no had this really pleasant experience with handling AGA/RTG on the same screen on a real AMiGA, and in some cases WinUAE does that better.
In the end, what it all comes down to is how one wants to use the AMiGA. In some cases I prefer WinUAE, in some cases i prefer the real thing. They both have advantages.