I know the Windows registry is a complicated thing so CCleaner may not be very aggressive on purpose. However, there are some things that CCleaner could at least notify us of. If a registry key contains a directory/path that doesn't exist then I would like to be notified of that. If a key contains no values I might want to be notified about that (aside from certain keys that are supposed to be empty). If a software key exists under HKCU\Software without a mate in HKLM\Microsoft\...\Uninstall then I might want to know about that too.
I understand this would create a ton of extra entries, a moderate amount being false positives, but this could be one of those checkboxes that is not selected by default. Also, I don't think any default action should be taken. Which keys to delete, if any, probably shouldn't be an automated decision.