Personal opinions follows:
WinUAE is GREAT for CPU demanding programs like 3D-rendering and DTP. I mean.... it feels like having a 68040 running at 1GHz or there abouts.
For games however..... I don't think it "feels" right..... screen is too "crisp" and so is the sound. Though this may be a problem of the gfx-card and screen, and of course the soundcard, not with WinUAE itself
So... what is the best option? For me, it's entirely up to the task at hand. for some things, I'll be happy to use the emulated Amiga. For others, I swear to my Real Amiga. It's what you prefer yourself... there's no conclusive answer, IMO.
My best advice would be "Try to run the same programme/game on both, and see what you prefer yourself"