I don't think it's really a budget issue. The type of 3d modeling & animation software that is necessary to create character spritesheets can be had at pretty commodity prices (sub-$200).

Personally, I would never try to do this kind of work by hand in 2D (not a talented-enough draftsman). But the grandparent is right...even in my clumsy hands, I can do a decent job working in 3D. It's just an easier workflow.

Now, style-wise, nice hand-drawn 2D animation is in a class of its own. If indie studios are sticking with 2D, I'd suggest it's frequently more a matter of style than price.