The fact that both games have issues could be down to the particular firmware you're running, or the Micro SD. You could try a few different things in order to get both working, which are:
- Try formatting the SD card. Sometimes when games have errors or do not function correctly, this is normally one of the best fixes in order to get them up and running.
- Delete the current version of the firmware you are running, and replace it with a newer version (if any), or use a freshly downloaded version of the same firmware edition. This used to happen a lot with my M3 Real and my R4DS, and normally this solution would work. Alternatively, you could try using the M3 Sakura firmware if you aren't already. That should play both Pokemon Platinum and The World Ends With You perfectly, because I know they both work without any hitches for me on that firmware.
Anyways, I'm hoping one of those ideas will work for you. Good luck and I hope they load properly. ^^