1) Re-sizing is an automatic procedure (Imagine re-sizing 2000 frames of handdrawn animation - I have a feeling you entire art department will leave the project, screaming)
2) Re-use of base models is a lot simpler (E.g. one "person" type 3D model can easily be the base of several different fully animated sprites).
3) It is a lot simpler to get a common style across the full set of sprites (lightning and shadows are consistent + materials may be re-used)
/Niels