The 9 Tomoe and Rinnegan are as far as we know identical to each other than the actual tomoes. Over generations, family lineage may change in the forms of looks, hair color etc. Kaguya didn't have children with a man who was identical to her. In other words, she didn't have children with a man who also had the Juubi's eye as that doesn't make sense really. When she gave birth, her children was born with the Rinnegan. Which most likely comes from the Juubi's eye with a combination of the Byakugan. There are two reasons I say this, for starters the Juubi's eye looks alot like the Rinnegan but only missing a single trait. ( Something that may change over a single generation ) The next thing is the color of the Rinnegan. The Rinnegan is pink/purple'ish in color and that may be because the original Sharingan was combined with the Byakugan. Whiten red too much and you will be left with a pink'ish color.
Also, Kaguya had both the Visual prowess of the Juubi and the strong body of her lineage. Sasuke only has the visual prowess of the Juubi, while Naruto has the body of Kaguya's lineage. Seperately, they are not stronger than Kaguya, but together they are stronger or at least just as strong as Kaguya.