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.