This patch fixed my saving issue on my M3 Perfect. I wasn't experiencing any freezes either until a moment ago. I've been playing for an hour and a half and after I raised my Caterpie a level it froze when I took 3 steps through the grass. Is this the kind of freezing everyone else is getting?
I've noticed that all M3 users, no matter which one (M3 Perfect, M3 Real, etc) are having saving issues. This patch fixes that for us. For those wondering, here is how I got it running on my M3 Perfect: 4xDMA, Force R/W, Trim Rom.