I compared the two, but I'm too spec illiterate to know which would be better. As far as I could see, the advantage with the Gen3 is the PCI-E 3, where the B3 only has PCI-E 2. That will probably just be something that will help in the future.... thoughts?
Battlefield 3 will be the main purpose of this machine, and I am installing a 64GB SSD, if that makes a difference.
B3 has the B3 P67 chip that fixes the SATA bug, and like you said, Gen3 has that plus PCIe 3.0 slots but you will need an Ivy Bridge CPU to use them at 3.0 speeds, otherwise they run at 2.0 speeds. Other than that, I believe they are the same. The Gen3 is actually $5 cheaper than the B3 on Newegg, so you might as well get it. If you are planning on upgrading to Ivy Bridge or beyond, then definitely get it.