Advantage:
Mainly one: AIR-FLOW. you will get much more air-flow, components can run cooler, and hopefully quieter
two?: more room for HDDs, if you are someone who wants 2+ HDDs connected to your mobo, even it is mITX, you will want something bigger than a minimalistic mITX case to hold them all.
disadvantage:
Size: this is obvious, you got an mITX case and you're using a larger case so one can say you're not taking full advantage of what you bought
cost: since you're putting it in a mid-tower case, most of which are big enough to fit mATX boards, you're basically paying more for the same thing. most microATX mobos are cheaper than mITX boards because it is easier to fit the chipset on the slightly bigger boards. in addition, many people using an mITX want "no compromise minimalistic" builds, so mITX boards tend to bundle in more stuff such as wifi, better onboard audio, etc. and it is easier to get a basic mATX board