At first I bought into all the MK hype, thinking that like any other match-up, it must be at least 70:30 in MK's favour (known as the "3rd commandment of Brawl").
However, much to my surprise after playing Ganon and experimenting I believe this match-up to be 80:20 in Ganon's favour! I know, I know, it may sound mind boggling, but bear with me and I'm sure you will think the same.
MK has speed, we all know this. But what MK lacks is power, a solid killing move, and most of all reliable gimps. As we all know, Brawl has no combs (see the "6th commandment of Brawl") so speedy, combo based characters tend to not do as well against characters with 4-5 solid strong hits for a kill. Not only this, but Ganon has very reliable gimps (the guaranteed Dair, reliable Bair, utilt, Wizard Foot, Ganon's hidden footstool jump bonus and Flame Choke suicides), just giving Ganon the edge he needs over Metaknight.
Now you may bring up that Metaknight has good range and the dreaded Tornado. Most people forget that Ganon has range to combat this. Wizard's Foot, Warlock Punch, ftilt, dtilt are all very quick moves with little lag and great range. Furthermore, Warlock Punch and Wizard's Foot can be used to outprioritise Mach Tornado. If you haven't figured out yet, Wizard's Foot is key to this match-up, much as fair is key to any Marth player. Wizard's Foot will help you gimp MK, has great range and can be used to beat Tornado.
This concludes my opinion on this match-up, it is a clear 8:2 advantage to Ganon.
