Okay. Let's say... We have 2 MOBO's... A and B
How do you determine that MOBO A is better than B?
For Intel they almost all have the same Chipset so what I look for when shopping is the heat sink on the VRM and the power delivery. I'm big into overclocking and you want something with a nice heat sink on the VRM because you really can’t change that on your own. Another thing that has caught my eye lately is the lack of right angled USB3 headers on a motherboard; I've seen them mostly in MSI boards. I terms of PCI Express layout I like to have three step spacing and one PCI E 1X slot on the very top for a sound card, so it doesn’t interfere with video cards. Really other then that, they are all very similar. Maybe different IO's say you want ESATA or thunderbolt. Another thing is right angled SATA ports but that should be on any and every board.
Depends on what you're looking for. It's personal preference really. If you're going for overclocking, the first thing I look for is power delivery and VRM cooling. If it's a media motherboard, I/O and integrated sound. Aesthetics can play a part as well. There is also expansion slots. If you have an old PCI card you want to use, obvious a board that supports legacy PCI would be better; if you plan on running an array of GPU's, PCI-e lanes play a role. If I just want to throw the CPU in there with some RAM and get going, the cheapest one that's known to be reliable is often the best. There is no one thing that makes one board better than the other, it's knowing what you want from it.