I think when it comes to shadow clones.
Naruto is a unique case.
There is an obviously difference when Naruto creates clones when compared to the likes of Kakashi, Jiraiya, or Sarutobi.
They place a good deal more control into thier clones and are clearly more durable than what Naruto usually produces.
The fact Sasuke could see a difference with his sharingan at the valley of the end, may simply be due to the fact he was pumping out a mass of kyubi chakra and as such finding the real Naruto as the source may have been rather easy.