Well it certainly isn't easy to upgrade one. But here are your options:

1. The Mac Pro six core uses the Xeon E3-1650 Westmere running at 3.5ghz. So it is a very decent processor
2. Unfortunately by default it ships with all memory slots full 4x4GB but at least they are using unbuffered ECC RAM DDR-1866. So to upgrade, you essentially have to start all over. There is a 4x32GB option that costs a whopping $1400. The reasonable OWS option 4x16 for$500. But note that this again fills all your slots. This is just standard RAM, so at Newegg, it is a little less. $112 for 2x8 Crucial, or$220 for 2x16 rDIMM (registered so about $450. Nice thing is that you can reuse the memory in say an 8-slot X99 board. 3. The disk was an anemic 256GB and it is very expensive to replace as it is a custom 4x PCI Express 2.0 capable of 2GBps. OWC sells a 1TB replacement for$900. That compares with using Thunderbolt 2 which is running at 20Gbps on each connection and there are six of them on the back (although some are doubled). What that means is that you theoretically could put something running at 2GBps outside of the chassis which is much cheaper. For instance a Thunderbolt 2 adapter is \$350 for the enclosure and that means you can swap your SSDs as needed. This is a good solution for storing data for sure.