I see two possibilities.
1. This all has to do with the series finale.
Kishimoto realized that Naruto was so much more powerful than Sasuke that there was no way that he could have the two face off without Naruto simply mopping the floor with Sasuke. Therefore, Kishimoto had to level the playing field somehow. By removing Kurama's chakra already inside Naruto, he essentially cut out all of the abilities that Naruto had to were specifically catered to defeating an Uchiha. For instance, Naruto's speed is back down to his normal level; Naruto doesn't have a protective chakra cloak that theoretically wouldn't be affected by Amaterasu (much like how Nagato and Gaara countered Amaterasu); Naruto lost the TBB, etc. This essentially resets Naruto and Sasuke to their levels prior to the War Arc, and makes up for the complete lack of development when it comes to Sasuke since he killed his brother.
2. This has something to do with unlocking their overall potential.
Somehow having the Yin chakra will make Naruto more powerful. Conversely, perhaps death is the final stage of awakening the Rinnegan. We do not yet know the details of how Madara was able to awaken the Rinnegan. We just know that sometime after his battle with Hashirama, he used Hashirama's DNA. However, every other Uchiha doujutsu requires some sort of mental anguish, and perhaps the Rinnegan requires the person to die.
