Personally I dont think either is better or worse, theyre simply different.
The biggest downside to Winuae in my opinion is the host hardware/os. Not that I have a problem with either Windows or x86 pcs, I simply like to have dedicated systems. Im not a big fan of using any VMs "seriously", so Winuae is no different. The massive speed available to (Win)uae is also a mixed bag. Great to have at times, but in some ways removes the "amiga-ness". Porting software for example.... when it'll compile with minimum effort, or a lack of amiga-fying/optimising the resultant software feels generic, and loses a little of that amiga flavor.
Having to launch an OS first, just to launch the "amiga" also makes it hard for me to focus on doing anything "serious" and as such any emulated environment for me always ends up just a "fooling around" playground. Amithlon is the exception here for me, but that's not really a "typical" emulator. Yes, you can strip back Windows and have it boot straight into amigaos, but Windows still does peek through at times. A pcs bios also destroys the effect a little, but that's becoming less and less of a problem as time goes on, especially with bios post times reducing nowadays (theyre practically non-existant already in some netbooks).
I think the fpga "amigas" have an edge in authenticity as things stand, and this isnt necessarily down to the software that defines either, but rather due to some of the points Ive touched on.
This doesnt necessarily make it better for everyone, but for some people its more important than the flexibility and speed a software based emulator running on an x86 pc provides. This of course also means that the reverse is true for others.
Different strokes for different folks as they say. Either way I think its great that the amiga will exist long after most of our real Amigas have gone to silicon heaven