Being better comes down to what your going to do with it. The shuttle solutions are, hands down, the faster solution, ITX is better suited for integration into a car though.
I think cost is pretty close when all is said and done, of course this varies greatly on which models you compare and which options you add. ITX has a slight advantage though particularly in terms of power supply if you don't spend $180 on an OPUS.
With shuttle you get a MUCH faster system, an integrated 3D card, Optical inputs and outputs, and I think the motherboard chipsets from intel and nvidia are much better then vias. The shuttle case is also extremely well made. With ITX you get a slower system but it takes less power, can be much smaller depending on the case you get, and doesn't generate as much heat.
You have much more flexibility with ITX since you usually buy the case separate from the motherboard. The shuttle comes with a case, very nice heat sink and is pretty much ready to go and very easy to setup, just add processor, ram, and hard drive.
When it comes down to it, if you can make the space or need 3D capability, the shuttle is the better option , get the ITX only if you can't find a spot for an 8x8x12 case.