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I owned both at a time (well, technically I still do...), and the compatibility of the games seemed pretty solid on both. Any problems I had was easily fixed but switching the patch option on/off (SCDSOne), turning off soft reset (M3DSR), and etc. I don't know about the newer games, but I've never had problems with either.
You probably should know that I sold off the Supercard to one of my friends because I liked the M3 better. The reason for this was that the Supercard, though it had neat features like real time saving and in-game cheat options, the thing was too damn hard to figure out. To even get the cheats you want you have to go through some kind of weird complicated process that should be really easy. The m3 supports 5 different formats, including the one Datel uses in their ARDS Software. You can easily make an UPDATED list of every game for the DS and copy it to your SD card no problem. Also, another major reason that I sold it off was that homebrew needed to be DLDI patched, something the M3 does on its own. I don't think the Supercard does that.
It's notable the the M3 DS Real has some drawbacks, such as some homebrew (2D games mainly) don't run, but there may be a work-around for that, and there are some things that the M3 Manual doesn't even mention you can do, such as GBA linkage. I've also heard something about built-in emulators, but I'm not entirely sure it's a rumor or a work-in-progress or what. If you're looking to buy another card, you oughta check out the CycloDS, as I heard it was pretty good with similar features, and I believe a new review came out just a week ago on gbatemp.net that you should look at.
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