I've been trying to figure this out for awhile.. The N5 will be amazing, but it's not as tightly integrated as Moto+Android imo.. I feel like Moto is more inclined to make it work and is more integrated with Google's idea then the Nexus Line now.. Specially since Googler's moved over to moto when the company was bought.
Nexus is a developer phone, it's great for tinkering and such, but in the long run its literally PURE android, which is'nt THAT great (I had the n4, and N7) Stock Android is great, but there's always something missing. Moto X is mostly Pure stock, but its got soo many addons that make it more valuable then the Nexus Line. and it runs GREAT, follows Google's Software Design (even if there's 2 different designs).. and adds onto their philosophy.
hope im not confusing anyone.
TL;DR- Motorola Mobility is more integrated with Google, then the Nexus Line.