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Erm, you know, you have an operating system in there somewhere with a plethora of drivers, services and auxilairy programs. Likewise, you may have a virus scanner, firewall, chat client or whatever running. It's not that PS would have al lthe computer by itself... That aside simply assume that PS is taking what it needs, but gets slower by tracking your footsteps while you work. If you don't want it to and think you can work without history and undos, then reduce those settings to the bare minimum, otherwise simply accept that things are as they are. Even on the most optimized system you can't defeat basic computational and mathematical principles. There may simply be too much going on and PS working its *** off to hold it all together. E.g. you may assume that nudging a layer should be quick, but it may not be at all because at the same time PS needs to calculate blending with a gigazillion layers beneath...
In addition to what Mylenium said, you did not state the number of processors, or their kind in the first post.
Imagine that you have a dual core processor, but use a filter, or perform an operation that can't be multithreaded, your efficiency will in this case will max out at 50%.
Some operations cannot be done on multiple processors, others benefit a lot from having more cores...
One thing that could speed up your processing, given the amount of RAM that you already have, would be to use a Solid State Drive as your scratch disk.
With 16 GB on tap, set your Photoshop memory usage limit at 95% or (if you're feeling conservative) 90%.