I was going to stay out of this, but hey it's all fun while we're waiting.
The past couple of releases the Note has always been compared to the Nexus phones, but I really think they are two totally different phones. I have had both because I'm a phone & tech geek, but for the average person it would depend on what you want out of a phone.
The Note series IMO is more of an all-in-one productivity type of phone. If you don't have a tablet and it's your sole device, having the split screen is nice. The S-pen is really nice for taking notes, help creating contacts and a bunch of other stuff. This is the phone I really would have loved to have when I was running my side business. The camera is also really nice. Samsung has done a lot with Touchwiz to make it appeal to the average customer, and I actually like some of those things. Between the two I would probably recommend the Note 5 for the average person.
The Nexus is a really good phone for media consumption and all the Google services. If you really utilize Google like I do, it's a far superior experience vs. the Note IMO. When I say utilize it, I mean use it for Gmail, Google plus Youtube, Google play, docs, pictures, and Play music & movies. A lot of Google stuff is in the cloud, and the Nexus phones from my experience work better for this purpose.
The Note can do all the Google stuff, but Samsung tries to push their own software and apps so the experience is not as clean or smooth. My Note 5 is periodically downloading & updating Samsung apps , most of which I never use. The Note 5 has it's own music app which I never use, as well as the video player.
Since the Nexus has been updated, battery life is pretty even IMO, and I'm saying this from my experience with the Nexus 6 and Note 5 since the 6P isn't out yet. I will miss wirless charging that the Note 5 has, but having a USB-C port helps alleviate that. I have a Chromebook Pixel and it's really nice to just snap it in with the USC-C and it charges very fast.
All in all I prefer the Nexus for the reasons mentioned above, the nicer build quality, fingerprint scanner, and running Android 6.0 stock in the 6P, it's the better phone for me.
Long post, I know, but that's what I think about the two phones.