One is a SATA-based SSD - the Mercury Extreme 6G, the other is closer to what the new Mac Pro has - it's a PCIe card with SSDs on it, OWC's Mercury Accelsior_E2.
To give you some sense of how significant the difference in speed is, I've borrowed a couple of different products from Other World Computing (OWC). The bottom line is that you're going to see a huge increase in speed either way it's just a question of what your budget will allow. There are different options available for Mac Pro-compatible SSDs, and we're going to look at two of them here: a SATA-based SSD and a PCIe-based SSD. But should you replace your Mac Pro with the new one? If you want to get as much bang for your buck, upgrade your aluminum Mac Pro with an Solid State Drive (SSD). Apple's new Mac Pro has some Mac users buzzing: the tiny machine appears to be crazy fast, and it's a total redesign of the system - replacing the giant aluminum box of yore with a tiny little black cylinder.