I agree with fishy_fiz that an AGA 256 color workbench is just not smooth/fast enough for use, at least for me either. Layer.library patched, Fblit in use and definitely configured properly. However...my system was using a monitor that required DblNTSC which eats a ton of bandwidth of the chipset as well. I installed an Indivision AGA MKIIcr but still kept color resolution at 32 colors.
Granted, I had mostly been using Amithlon (1680x1050 @ 32bit color) and WinUAE 1680x1050 @ 32bit color) displays for AmigaOS, so switching to an Amiga 4000D/T the 256 color displays on those were horribly slow.
If I was running a stock setup, I'd lean towards 32 colors with FBlit to keep everything more responsive.
