The better 3D packages pretty much all have plug-ins, or included settings, that produce good-looking line art from 3D models, complete with cel shading. I've seen these work to great effect on mechanical models, though most of the organic models I've seen still look a bit 'off,' especially when animated (although given that it's an order of magnitude harder to animate organics in 3D, anyway ).
And I agree that when it comes to characters, it's often more believable - or at least less off-putting - when characters are somewhat less realistic than when the modelers strive for ultra-realistic characters. Our minds are too familiar with our species and its abilities and quirks - when something isn't quite right, it stands out like a sore thumb to our minds and pulls us out of the experience.
So I take it from your first paragraph that as of yet there are no wholely convincing plug-ins to convincingly make the characters less "3D-ish"(for want of a better term) and make organics appear to have been drawn more conventionally.