Before CTDS was announced, I was seriously considering doing this to play CT on my DS. Good thing I didn't. Yeah, it sounds like it doesn't really work all too well... Now, how To put Mother 3 onto a flashcart is the question...
I have my own flashcard now, but a while ago, I borrowed my friends, then tried every possible DS-SNES Emulator.
There was one that took the nes rom and compiled it into itself, making a new nds rom, there was one that pulled in the rom while being run, another that used a menu system to pull multiple roms in folders, etc...
I had great success with other SNES games. I had no problem with anything... but chrono trigger... it seems that none of them can emulate the physical cartridges that the game had....
I wanna get CTDS, but I havent had the time to go out and get it... Nor do I want to pirate something that I would gladly pay for.
Edit: I did get it to work-ish on one emulator, but the sound didn't work, and every sprite was messed up a little, especially background layer sprites.