I just bought a Trek Fuel EX 9.8 XT. Love the bike, but there's one small puzzle---the bike comes with a 29x2.6 tire on the front and a 29x2.4 tire on the back. I checked the website and it's advertised this way, so it wasn't an error or an out-of-stock situation when it was built.
I'm mildly curious as to why they'd make this specific configuration decision.
I like running something skinnier on the back. It's less likely to suffer sidewall damage and it doesn't squirm as much in hard cornering. A bigger tire in the front is nice, as the large volume tire dampens the trail chatter better and helps maintain control.
I run a similar setup with tire size. This is for the same reason rear while drive cars often have skinnier front tires.
It's is for the purpose of reduced grip. On a rear wheel drive car you would rather have more rear grip than front as you don't want the car to spin when applying power. On a mountain bike you would probably prefer the rear to brake traction before the front.
Fat tire in the back makes sense for hardtails, but for full sus bikes it is a good compromise to sacrify a little bit of grip and damping for rolling resistance (and tire clearance). Most grip is needed up front, so large, grippy tire up front.