To me the choice is rather simple: the original hardware.
WinUAE is way too buggy, and emulation isn't synchronized in such a way that it really feels like running a real Amiga (especially not when running Workbench). Some things emulates way too fast and some things go way too slow which makes Workbench feel rather... 'surreal'. On some systems WinUAE seems to behave, on others it simply refuses to do pretty much anything the way it was meant to be done. Annyoing, to say the least.
However, I have been nothing but impressed with the performance of WinUAE, speedwise. On my old Compaq Presario 350MHz, 192MB RAM, running Windows XP... every single game I tried to run, OCS/ECS aswell as AGA, ran in perfect 50Hz/60Hz with no frameskip whatsoever (perfect only when having turned on VSync, of course). The only thing that disturbed me back then, game-emulation-wise, was Windows inability to show PAL-screenmodes on a CRT monitor, because using the 'filter' option, streching out the screen on a higher resolution, let's say 1280*1024, isn't really the same thing as the real thing.
Besides, when using the 'filter' option while running WB in native screenmodes, it sometimes feels like the JIT-emaultion is turned off. The system slows down to a crawl, and this have been true for all of the different systems I've tried running WinUAE on.