If you are determined to play the DS version via emulation and want the "better" experience, bypass shady QR codes entirely.
Square Enix released an updated version on mobile devices. chrono trigger ds rom qr code better
For those who still want the actual DS ROM on actual Nintendo hardware: If you are determined to play the DS
The most efficient way to play DS games on a 3DS is via TWiLight Menu++. This homebrew application allows your 3DS to emulate the DS firmware, meaning you can play ROMs directly from the SD card without needing a flashcart. For those who still want the actual DS
The QR Process:
Square Enix eventually ported the DS version's content to PC, iOS, and Android. The modern "Chrono Trigger Upgrade" on Steam includes the DS cutscenes, the Dimensional Vortex, and the re-translation.