Yeah, something is definitely wrong on your end. I've been running BrawlEX just fine since day one on USB Loader.
As for your reasons for the way you rig, they're valid. No need to be on the defensive. I just think it's kind of a waste to use your time to rig a character (it definitely takes a while if you're doing a quality rig) for it to only work with one moveset.
EDIT: Project M also works with USB Loader (but you need to know how to adapt it since the creators meant for it to be played with the disc always). Anyway, you CAN use stuff from it even if you can't play it...
Well, YOU can do. But people who download your model won't be able to use with whichever moveset they want.
I'm quite sure that you can change translations on the animation file itself, so there's hardly need to alter the basic skeleton rig, unless of course the model is going to be ONLY specific for that PSA (like Mewtwo has a modified Lucario skeleton to suit the moveset better), in which case if anyone ever wants that model over the basic Lucario skeleton they have, well... to basically re-do the rigging.
Why would you do that? Editing the boneset, I mean. Well, sure, whatever floats your boat, but having a modified bone rig only makes it so your model won't work properly for any other PSA, and even the default movesets at vBrawl/PM.