Reportedly, Nexus 6 was supposed to have a fingerprint scanner on the rear side, the dimple on the backside which is now a Motorola logo. This information is confessed by the former Motorola's CEO Dennis Woodsi recently in an interview.
Back in 2011, Motorola was set to launch it's Atrix 4G smartphone with fingerprint recognition using Authentec. But after a year, Apple bought Authentec for a price of $356 million. Earlier Authentec was in Woodside's Judgement which is the "second best supplier" and the only one available to everyone else in the industry.
However, Apple acquired the best fingerprint sensor manufacturers in the market for some millions and consequently Nexus 6 was not able to get the bio-metric authentication.
There were other bio-metric authentication technologies in the market but not as good as Authentec. So Motorola dropped the idea and housed it's logo on the dimple.
Other smartphones like HTC One Max came up with alternatives of Authentec, but they ended up with slow and buggy experience. Probably, Google and Motorola made a right decision in not using the bio-metric authentication alternatives in it's flagship.
On the other hand, Apple's Touch ID fingerprint scanner works fast and is accurate, moreover it is equipped on the front-side of the phone. Although, it will be a good feature to see a fingerprint scanner on the Nexus 6 but Apple killed the idea by purchasing the best in the industry.