what is the difference between them
Comparing the two, the Extreme 3 has a 8-phase power delivery vs. the Pro 3 which has 4-phase (better, more stable voltage when overclocking on the Extreme3). Best explanation I've ever seen:
Also the Extreme 3 uses Nichicon Fine Gold series audio capacitors while the Pro3 uses ELNA audio capacitors. You probably won't notice a difference here.
But probably the biggest difference is the PCIe slots. The Extreme3 supports SLI/Crossfire with its two PCIe 3.0 x16 slots (x8/x8 if both used) while the Pro3 only has one PCIe 3.0 x16 slot. The Extreme3 then has 1 X PCIe 2.0 x1 and 3 PCI slots while the Pro3 has 3 X PCIe 2.0 x1 slots and 2 X PCI slots.
The Extreme3 has an IR port header, the Pro3 doesn't but does have a TPM header - you probably won't be using either of these. The Extreme3 has 3 chassis fan connectors (1 X 4-pin, 2 X 3-pin) while the Pro3 has 2 chassis fan connectors, both 4-pin. The Extreme3 has an optical S/PDIF out audio port while the Pro3 doesn't.
So the biggest difference is SLI/Crossfire support on the Extreme3. Otherwise the Extreme3 is a more premium board with slightly better features.