I have used only mATX boards for over 3 years now,
and don't regret it a bit. Again, if you're a gamer (what I'm not) - it could be different.
The downside to mATX boards is the lack of slots, especially PCI slots. The P5E VM-HDMI only has 1 PCI slot but has two PCI-E slots. Some people like to put lots of TV tuner cards into their system and those have traditionally used a PCI slot. Nowadays many of the newer tuners are USB or PCI-E so you could get away with this board. I came very close to getting this mobo for my latest PC but I wanted more than 1 PCI slot as I wanted to reuse an existing Hauppauge PVR150 analog tuner card plus a Kworld ATSC OTA HD tuner card, both of which use PCI slots.
The other downside would be if you want to use a higher end passive video card, like a Sapphire HD 3850 Ulitmate, then it may take up so much space in your case due to the large heatsink that adjacent card slots are not useful. But you don't really need this video card unless you are doing some gaming - I am adding this card to my existing HTPC as I needed a better card for BR playback plus I do play some Guitar Hero III which was causing my 7600GS passive card to choke.