Amithlon IS loads faster than WinUAE and will remain so wether you believe it or not - your Amithlon installation is broken.
Make sure you`re using a supported graphics-card and not one that only works in vesa mode. Make sure that Amithlon supports ide dma on your motherboard. Install all the patches and the x86 memcopy routines.
Don`t claim the sky is green unless you have proof that isn`t just down to {bleep}-error.