Just a quick question I should ask. Do you think (even though its a 12-core) my low clock speed (2.4ghz) can just be the issue?? I originally had a 6-core Mac Pro @3.33GHz but sent it back for this machine thinking I was getting a faster system.. Was my decision making process wrong?
12-core machines are only worth it when using software that can use all 12-cores. If they cannot utilize all 12-cores, then the faster clock speed single CPU would have been a better choice. Depending on the software you're using, it could be part of the bottleneck.
Try converting your MP4 to ProRes and test playback. See if it improves your experience. I've edited those converts on MacPro1,1 and MacPro2,1 machines recently - both faily "stock" except for storage upgrades. Even had original X1900s. Got very good real time performance on both with FCP7.
There's a few threads about the 12-core 2.4 vs 6-core 3.33 in real world performance. Search and take a look through them. I'd probably go with the 3.33 as an overall machine, unless you're doing a lot of 3D work or heavy AE renders. They can take advantage of more memory available as well, which can help when speed matters.
The 12-core needs RAM to function at peak performance. Wouldn't rule out an upgrade there at all. No ideas about what you're currently using.
The 6-core 3.33 is a great machine still. If it natively had USB 3 and PCIe3 then that would be enough of an update for most people to have a really good workstation. Still wouldn't be enough for everyone, but those people are on PC workstations already, or really close to switching. Tying up a PCI slot for a USB card is tough for many and would mean an expander case to really make it work. If I'm going through that hassle, I might as well build a hackpro.