I have both an S7E and a N6P and the size is the only thing that really bugs me about the N6P. It's a great phone otherwise. However, being obsessed with the shiny shiny I went ahead and bought an S7E.
I have to say that it's the most comfortable phone I've used. The size is perfect and the in-hand feel is like holding liquid glass. It sits nicely in my pocket instead of almost poking out like my 6P. So it's a decent improvement in terms of size.
The software isn't quite as streamlined as stock Android but there are some handy features in there and some improvements too. It's fast and there is little lag. With a Material theme it looks pretty good too. It's certainly not annoying to me, but YMMV.
The main thing that makes me question keeping this phone is the state of Android updates. I know that my 6P will get the N update within a couple of weeks of it launching. The S7E may not get it for 6 months if Samsung's track record is any indication. As a total Android nerdlinger, that really bugs me - but the S7E is just so nice that I don't really want to send it back either.
TL;DR - yes the S7E is better, but how much better it is depends on your love for stock Android and getting updates. And your bank balance. The N6P is probably better value overall. With the S7E you're paying a premium price, but you are getting a premium product.