There is this 3d animation program called Maya. It's said to be the industry standard for 3d animation, just like Toon Boom is for 2d animation. Just imagine if there were bronies that would animate with Maya, it would certainly give SFM a run for its money. But let's face it, the vast majority of bronies animate in Flash for 2d and SFM for 3d. There is one particular artist who has used Maya to render MLP character, here's a pic.
Just imagine if someone could animate with this, they'd be the 3d version of Duo Cartoonist!