Aren't there already ballistics tests for this sort of thing, to match up the marks on the bullet with individual guns?
IDK, but I've seen it on CSI: Miami like a bazillion times.
Also, there are situations where a crime can be committed with a stolen gun. If I steal another person's gun, commit a crime with it, and return it without the person I stole from ever finding out, then they can trace the bullets back to his gun and look, they're instantly a suspect in something that they weren't even involved in.
Also keep in mind that a smart criminal will attempt to get rid of their weapon as soon as they're finished using it. This could mean selling it on the black market through a fence. Since the black market is completely unregulated by these laws, the gun that was used to commit the crime essentially becomes undetectable and disappears off the radar entirely, until it shows up with another owner later.
And what's to stop people from finding more mechanical ways around this? I agree with Damen, this only hinders the law-abiding gun owners.