This is MY personal feelings on the matter:
First, Nexus phones don't, technically, come with 'stock' Android. Stock Android is something you can find if you install a bare-bones custom ROM built from Android Open Source Project source code. There are some differences between Nexus builds and AOSP builds (outside of the obvious Google stuff they include). BUT... that being said.... There is virtually no functional or visual difference between a pure 100% 'Google-free' build of AOSP and what you get on a Nexus phone... apps and Google Services framework aside, of course. But take a stock build of Android, flash the latest Google apps package on it and you'd be hard pressed to tell the difference.
OK...
I've used several phones over the years from a few different OEMs and the closer they are to basic, unaltered Android, the more I like them. I prefer the clean notification shade, the straightforward layout of the Quick Tiles and Settings windows. Inter-app linking pop ups, etc. They all just seem to look more polished or OS like on these.
And they seem to run better. The more the OS has been fussed with, the more things suffer. Stutters and hiccups... clunky animations of occasional frame drops. The two best phones I've owned have been the Nexus 5 and (after 5.1.1) my Nexus 6. Even the humble little first gen Moto G that I have runs well for its extremely meager specs. Using anything from LG or Samsung (even the latest ones), you can almost physically feel it struggle under the weight of far too much overworked code. And Google sprinkled some additional magic pixie dust into 6.0... I can dual-boot my Nexus 6 and there's even an noticeable improvement bettwen that and the latest 5.1.1 stuff.