Google could have worked with Motorola to integrate every shortcoming people could point out as lacking from the Nexus 6 as implemented vs the competition (above points on camera, IR blaster, fingerprint scan, curved edge, 3D camera, physical keys, on and on and on...) but if they had they'd have been scorned for the price the phone would have to come out at, and then the phone would be one-upped by the next Johnny-come-lately device to have 95% of the features at a much lower price.
No, the Nexus 6 doesn't have the best possible camera hardware in a phone, but what it does have is among the best - and the fact that Lollipop allows devs a lot more control over the camera's operation should afford substantially better performance through well-developed 3rd party apps than that which we've been given from prior iterations operating under tighter reins (unless the vanilla API is exceptional to begin with).
For my part, I'd never turn down a better camera in a phone, but there is a point where I'll acknowledge that it is 'good enough' and that the additional cost required to implement a better camera in a phone, if I really want a better picture, would be better invested in a dedicated camera. At any given time there will only really be one 'best camera phone" and that one will always yield that title to a newer release in short time.