ATX would have more options on the motherboard: IE: suports more RAM(or more RAM slots), more PCI(x1, x8, x16) slots, more fan headers, usb headers ect. You should compare the 2 motherboards to make sure it has all YOUR required inputs and such, keep in mind for future upgrades such as if the ATX-micro only has 1 pci-e x16 slot and the ATX has 2 pci-e x16 slots; you wont be able to SLI 2 graphics cards on the micro(this is example) but you will be able to SLI 2 on the ATX. Its all about YOUR preference and what you want to be included with your motherboard.
It doesn't necessarily mean bigger motherboard is better just all about preference on what you want to hook up on the motherboard; I started with a Micro ATX in a smaller mid case, 3 months later i ran out of room and decided to upgrade everything except the processor so i now have ATX with a bigger mid case.
So base my reasoning on the only reason i would go Micro-ATX would be lack of space in my case but since i have plenty of room for other components i dont need a micro-atx i can use ATX no problem.