Originally Posted by Numinous
@ apocalypz: only the Zetsu coat would modify his chakra signature of all the arguments you made and it would be a non-issue if Minato was a sensor, considering Ao and Karin were able to distinguish different chakra signatures within the same person (Danzou and Naruto respectively). Considering that, if he was a proper sensor, he WOULD know Tobi was Obito. Since he didn't, the logical thing to assume is that, if he senses chakra at all, he's very inexperienced on the matter.
Mainly due to AO's eye was he able to see the color and difference in Danzo's chakra. Him being a sensor helped but his eye was the factor in that case.
Also I could be mistaken but I was sure AO said something of recognizing the color in Shisui's eye. He recognized it because of their past battle. If assumed Obito already had another Sharingan wouldn't that eye have a different chakra color as well? Obito from a color stand point would show three chakra signatures.
In Naruto's case if you're a sensor and you can't tell the difference from a really warm chakra vs a really immense dark chakra...than quit your job...Her comment was just that Kyuubi's chakra was similar (sinister) to that of Sasukes. The main feat Karin had in that bout was noticing the chakra levels within Danzo's jutsu. She only knew of the sharingans because she counted them, and she was unaware of Hashi's cells. Like I said her help came when she noticed the number of seconds it was before Danzo could use Izanagi again.
Going by the actions of Obito...Minato's best assumption was Madara.