There are couple things to keep in mine.
Are you planning on add on card? (not really needed since most mATX mobo already has all in 1 feature.)
How many serial device you are going to use? OBDII, IR sensor, Relay card ( I need 2 ports. USB->Serial sometime don't work)
Capable of "Resume on power failure". A nice feature to automatically start the PC when you feed power to the PSU (If the PSU doesn't have the automatically "push" the power button for you. Opus PSU do this).
The 2 MSI is okay, but I would suggest you take a look at the BIOSTAR M7NCG 400 as it has some function in the BIOS that work nicely with AMD Mobile CPU. I have Asus A7N8X-VM/400. A nice board but PITA for AMD Mobile CPU.
BTW there are several threads regarding to "good microATX mobo" in this forum. So look up those thread as well.