They are superior in some ways. They have disadvantages too:
-Take a long time to install
-Only one per title ID (for example, you can't have Alpha Sapphire and Star Sapphire installed at the same time)
-Saves are locked to the console, whereas card-2 .3DS files are portable.
- use one of the many tools and the installs dont take that long
- valid point, first one i have seen.
- not hard to use jk's save manager or one of the other save managers to move saves to a diff system