Micro ATX is a smaller version of an ATX Mobo. Most ATX Mobo's have 7 expansion slots (PCI-e, PCI, etc.). Most Micro ATX Mobo's come with 4 expansion slots, so you are only limiting your possible expansion capabilities a little. Quite a while ago it wasn't uncommon to have several of the expansion slots used for a dedicated GPU, Sound Card, Network card, etc., so having more expansion slots was a good thing. These days most Mobo's cover all of the necessary bases. You have onboard Sound, even onboard GPU (which is integrated onto most CPU's these days), and even 1 or 2 network connections. Most Mobo's only need RAM, CPU, & a HD to work as a fully functioning computer.
ATX Mobo below w/7 expansion slots:
Micro ATX Mobo below w/4 expansion slots:
So what ends up happening for most people, is you can get a Micro ATX Mobo and save on the cost of the Mobo/Case, because you wouldn't need a bigger case to hold the smaller Mobo with. There is even a small Mobo (Mini-ITX) that only has 1 expansion slot and thus limits your upgrade/expansion capabilities.
So you can decide on what works best for your situation, but 98% of people will be fine with at least a Micro ATX Mobo.