These phones both run some very similar software. Of course the Nexus 6P is pure stock Android just as Google builds it, being a Google device, but Motorola keeps their phones closer to stock than anyone else. They refine it with added features like hands-free voice controls, and other things, not cover it with skins like Samsung.
The Nexus 6P already runs Android 6.0 Marshmallow, while Motorola just announced today that the Moto X will get an update, but we don't know when. Likely before the end of the year. Another thing to consider in terms of the software all some of the additions the Nexus 6P has. Like the fingerprint scanner for better security, easy logins, payments on the Play Store, and better Android Pay features. The Moto X doesn't have a fingerprint scanner, but can use Android Pay thanks to NFC. Both phones have a lot to offer, nearly stock Android, but one obviously has more choices and the latest software, that's the Nexus 6P.
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