While I was in the shower last night, I finally fell out of the denial stages of the limitations of the .3dsx format. .cia format homebrew has access to almost everything(except stuff that requires kernel access), and it's only limited by the fact that there's no kernel access yet, and a lot of the stuff that would make for better homebrew (the svcControlProcessMemory stuff) isn't implemented yet.
I do agree that there needs to be a standard format so that developers don't have to supply all 3 (dooes anyone even ship .
3ds homebrew anymore?), and worry about which format is limited in which way. Unfortunately, it looks like .cia is still the better choice, unless ninjhax's predecessor has a way to gain access to all SVCs and service ports.