I'd say its mainly personal preference and what the intended purpose of the rifle will be.
My opinion is that if you want a round that you can use for plinking, home defense, or small game hunting, go with the 5.56. Fairly inexpensive bullets and magazines, will keep you shooting longer and cost you less than with the larger calibers.
If your going to be using the rifle to hunt midsize game, i.e. whitetailed deer, mule deer, etc..., choose the larger calibers. Keep in mind availability and price of ammo and magazines.
I myself opted for a 5.56 model, mainly because it is the only caliber that my department will authorize and I can shoot it for free. I would love to have it in 7.62 NATO, but under the above circumstances and the price of ammo, it would be more of a safe queen than anything. Theres no fun in having a rifle that you cannot afford to shoot and have a good time with. Just my :2cents:
Jon