Well, it wouldn't necessarily be impossible to do a stereoscopic film with traditional animation, just look at the Studio 4C and SHAFT Kid Icarus shorts. But really, if he wanted to do 3D that badly, I think he should have chosen an aesthetic more fitting for the medium.
I mean, for a recent example, just look at the .hack//The Movie trailer. The designs have a clear anime feel, but it's shaded and animated in a way that takes advantage of computer-generated animation's strengths. I don't think it's the best-looking thing ever but it sure looks a whole lot better than that 009 Re:Cyborg movie.
I think you'll find that the .hack movie has "real world" character moments which look even worse than Re:Cyborg. The difference between the real world scenes trying to look "anime" and the in-game scenes looking "game CG" are even greater when in motion. So this is something all studios need to improve on, and not something exclusive to Re:Cyborg.
Some examples: