A couple of things:
In my experience, WinUAE is faster than FS-UAE. FS-UAE is not bad, but WinUAE is just a little better. I believe that FS-UAE is based off of WinUAE emulation code anyway, so FS-UAE is always catching up to WinUAE. On my old single core PentiumD computer I was able to get an amazingly smooth, super fast Amiga experience (faster than 060) using WinUAE. I absolutely loved it - and I was using it for productivity work like Lightwave, PageStream, MIDI music sequencing, ImageFX, etc. besides gaming.
I have since switched to Linux and now my only option is to use FS-UAE. While it's not bad - it's certainly not as fast as WinUAE. FS-UAE only recently properly implemented JIT. Also, it has problems with the Intel graphics chip on my motherboard (WinUAE under Windows XP didn't) and so the rendering of RTG screens has some latency and choppiness (I can see a lag in the mouse pointer movement) whereas WinUAE under Windows was absolutely perfect. I therefore keep a dual boot system and one of the few reasons I have to boot anymore into Windows is to use WinUAE.
I hear that some Linux users install WinUAE under WINE because it's faster/better than FS-UAE (even though WinUAE takes a bit of a performance hit being run through WINE).
Besides using JIT, your emulation speed will be GREATLY increased if you use the special WinUAE Picasso 96 driver from withing AmigaOS when running in RTG modes.
Also, try playing with the graphics rendering modes in the FS-UAE settings. The OpenGL modes, etc. Some of these are much faster than the others.