Could it be that software is written better for PowerPC? PowerPC systems seemed faster, but that was before all the software crud of the late 90's and 00's starts getting added. (Mandatory on Windows, optional on Amiga).
The machine (PC or Amiga) will slow down when a piece of software tries to overtax one of the components... CPU, memory or graphics.
If the OS is well tuned and there is no buggy software you will have a nice running machine. Trying to tune a modern OS would be a mammoth task and take several years to learn.