The original one is full ATX size, the other one is microATX. This isn't really a problem, but if you wanted to overclock the CPU, I would go for the first one as full ATX boards usually run slightly cooler and have heatsinks on the MOSFETS.
Also, and more importantly, the Extreme3 board has PCI-E 3.0 support. Not only does this mean you can use the new GPUs (when they come out) properly, you can also use Intel's Ivy Bridge CPUs coming out next year.
In short, the original one is better