If you want to try to put the computer in a space the Micro ATX won't fit, but the Mini-itx will, then that is the biggest reason.
I am putting mine in a 7x7x2 1/8 box, that means I have to go with mini-itx. Power requirements and heat are two other reasons you touched on also.
If I had a place to put it, I would go with a Micro-ATX board. Cheaper, better performance, more options. But I am impressed with the ME6000 that I got, better than I had expected. It is obviously not going to match a 2600+. It will do everything I want it to do.