Size is the advantage of a CR2 over a CR123A, as Storl said. For example, the Nitecore EZ 123 has a volume of 20.89 c^3, while the EZ CR2 has a volume of 17.32 c^3. About a 20% difference. Not a huge difference, but in our ever-bulging pockets these days, the extra size (and weight) of a 123 sized light can be a deal breaker.
If you can deal with the size though, a 123 sized light will almost always be brighter, and always will have a longer battery life. 900mAh capacity of a CR2 vs 1500mAh for a CR123A. 40% increase of overall output for a 20% increase in size is worth the sacrifice in pocket space for some. Batteries are usually the same price too.