Board Thread:Theories and Speculation/@comment-26118325-20150227103217/@comment-26118325-20150227135818

You would think that rinnegan has at least a limited ability to see chakra through smoke.

Nagato can't see through smoke but maybe he can't use the rinnegan's full visual power since he is a transplant user. It is said only a original owner of the rinnegan can use its full power which could include things like seeing chakra points.