Most Pci-e cards use a 3rd party controller (ie such as marvel) that does not provide optium performance. With the agility III, the diff between running it on Sata III vs Sata II will not be a big diff in real life performance - benchmarks yes. Myself, I'd probably skip the card upgrade.
The biggest diff will be in sequencial read/writes, which are the least important matrix for a OS + Program drive. It is the random 4 k that are important.
Your choice on getting a new MB, it will provide USB3 and Sata III. Is the benifit worth it - hard choice interms of $$$ vs performance boost.