An alternative is to look at the [sys_update_xml] and try to collate changes from there - essentially, this is what an update set is, but it could be a large amount of work for very little returns.
Cloning instances is free - I'm not sure why there is a restriction on it. I'd also say that people in your organisation making changes without opening an update set to record those changes are not following best practise - we discuss this on many courses (Sysadmin/Advanced Admin/IBC/Scripting) and their benefits, so it sounds like poor change management is leaving you in this position.
