1. Some phones will not charge when using MHL - or maybe it takes a different, split cable. Obviously this isn't a problem when you have separate HDMI and USB ports.
2. MHL for the GS3 is different than every other due to deficiencies in MHL. Samsung had to change it to make it good. I've never heard of deficiencies with MicroHDMI. I think it had to do with audio. This means two things, A. MHL cables are not all the same, B. Most MHL connections probably are not as good as MicroHDMI.
3. MHL cost more and are just not very standard, as eluded to in the previous comment. You can get a 10 foot long MicroHDMI cable from amazon for about $2.50 with about $2.50 for shipping. It looks like MHL cables are usually in the $15 range. I use the same cable with my Droid X, Maxx HD, BB Playbook (got it for free but it deserves much more credit than it gets), and Flip HD. That's pretty nice when my young daughters want to see an animated storybook app on the TV or we want to show home video from the Flip HD. I've even used the Playbook to watch NCIS off the networks web site on the TV.
I really wish all companies would just use MicroHDMI and kill off MHL.