Google/Android Flagship

Hey guys, I'm looking for advice. I've had the iPhone 4 since October 2010. I considered myself quite an Apple fanboy at that boy, and was for quite awhile- till Apple stopped innovating. I think the fact that I started using Google for literally everything (especially Google Drive. Google Drive is amazing) didn't hurt my transition to Android fanboy. Anyway, I'm well past my contract expiration date, and am looking at getting an Android of the flagship nature. This seems to be an exciting time, with the Moto X and new Droid phones coming out, as well as extremely well featured and well established phones in the S4 and One already gracing the market. However, I am looking for the pure Android experience that so many talk about. And it seems that this pure Android experience can only be found in the Nexus line as well as the S4 and One Play additions. But I'm slightly confused as to where Motorola and the Moto X fits into the picture. If Google owns Motorola, will all Nexus devices start to become manufactured by it? Will Motorola phones become the Android Flagship? Do the recieve the OS updates like Nexus products in the future? And most importantly, are they given the pure android of the Nexus line? Or does Motorola have its own skinning?

I hope you all can help me answer some of these questions, and point me in the right direction. The Moto X really excites me, but I don't know if it's the right choice, and answer to the complications of new Android updates.