Well personally I love stock android , would I let that fact alone dictate my choice of phone though , well No .
Iv had numerous devices over the years and the one thing that Stock android has always given me is great Ram use vs say a Samsung which always tends to hog the Ram use (granted I have not used the new S7's this year as yet) and quick updates . A perfect example last year was when the new Note came out and I was seriously considering one as Iv always liked the Note range , but when I compared the Ram use side by side with my then Nexus 6 there was a huge difference in the amount of free Ram available when opening numerous apps or internet browser pages .
Im currently using a Moto X pure and as user experiences go it has been one of the best devices Iv ever used , Iv not once had to worry about apps closing because of poor Ram use , lagging etc etc etc . The Mate 7 I had last year was also pretty good, though Huawei's skin does take some getting used to .
So personally while I would prefer stock android as in the nexus or Moto range I would not write off any of the other manufacturers just because they have their own skin . I think ultimately one has to look at what the device offers as a whole rather than just does it have stock android or not .