It's funny how people's way of thinking differs so much regarding this issue!
I personally prefer .cia files because I don't like clogging up the Gateway menu with homebrew that is hopefully going to get updated quite regularly, and .cia files can also be used by people who don't use Gateway and similar flashcarts (such as people who use CFW). I understand that some people like the fact that .3ds files can be drag-and-dropped, though.
I was a supporter of .3dsx files at first but I've come to view them as problematic. We have to keep our EmuNAND on 9.2 just so we can still use the Cubic Ninja exploit. This is made all the more frustrating by the fact that there's no .3dsx loader in .cia or .3ds format. I understand that people using the Cubic Ninja exploit can only use .3dsx files however. Ultimately somebody is always going to lose out.Most homebrew is distributed in all formats (.3ds, .cia, .3dsx, .elf) but there's always a couple that are only available as .3dsx (useless for people using 9.3+ without Cubic Ninja), just .3ds (useless for people without a flashcart) or just .cia (useless for Ninjhax users).
If all homebrew was in .3dsx and there was a loader we could install as a .3ds or .cia file then it would be a reasonable compromise to ensure maximum compatibility with all existing exploits.
