I would agree in general that a Mac Pro is mostly I/O constrained. This is partly down to it only having SATAII drive bays, so even if you stick a fast SSD in one of the bays like an EVO 850 it can be limited on speed. It is possible to fit internal SATA cards which support SATAIII and these can either be of a type on to which you directly fit a SATAIII 2.5" drive, or you can get a special kit which 'converts' the internal drive bays and then run cables to a SATAIII card.
Note: Using a PCIe SSD or PCIe SATAIII card may mean any drive attached to such a card might not be bootable in either OS X or Boot Camp, it depends on the card.
I have a 1TB SSUBX type PCIe SSD (the very fastest) and the biggest delay in booting is the POST (Power On Self Test), actually loading the operating system takes just seconds.
Other aspects to address are the amount of RAM - you want at least 16GB, more is always better, a faster video card - which you have done, USB3 ports - which you have done, and it is also possible to replace the standard WiFi/Bluetooth cards with newer faster ones which can support Yosemite's Continuity feature as well.
The beauty and curse of the classic Mac Pro is that you can keep throwing money at it to add new better components, even things like 10Gbps Ethernet.
I have done a fair few of these options already on my 2010 Mac Pro 'because I can'. I am currently considering but waiting for more choices the possibility of adding USB3.1 - there are some cards already out like the ASROCK, and a UHD Blu-Ray drive when/if they become available.