I think it really depends on the processor. If you have a processor family that is fairly high voltage and a big heat generator, then MATX probably won't work very well. I recently ran into that problem with an FX-8350. I got a killer deal on it, but my Asus board just couldn't handle it like it needed, even though Asus said it would. It barely met the requirements and the least little thing would throw it over. I ended up having to get a full ATX board to find something that would handle it. Before that I had a FX-6300 in it and worked great though. Like I said, it is really determined by the processor.
As for budget, I found an Asrock ATX board that was only about five dollars difference in cost than the MATX boards. So the...