<p>Just remembered something: When Nagato used Rinne Tensei, all the souls of the dead villagers (including kakashis) came back from the mouth of the Enma statue! So what if actually, the souls of everyone who is killed by a Pain go into Enma's 'territory' first instead of directly into pure land? This could be exactly the in-between stage Kakashi was in, allowing him to remain conscious to some extend. Also, if i'm not mistaken, didn't Kabuto mention he would have Nagato kill Naruto and Bee to then 'store' their souls inside the Enma and later revive them...
</p><p>Speculative i know, but it may be a possible explanation for why Kakashi was conscious and Edos weren't.
</p>