To "fix" the slowdown problem:
C:SetPatch QUIET SKIPROMUPDATES=exec.library
This will disable the slow exec written in C (so you use the older and faster assembler version).
Patches that is a must (assuming you got MMU and AGA):
FastBlit
FastText
BlazeWCP
MMULib
Using SmartFileSystem (SFS) will also speed things up significantly (especially sys:). AddBuffers will also help. Using FFS is generally not a good idea since it is unstable (cannot validate large HD's) and unsafe (write errors).