To me, the Note and Nexus lines are totally different phones, each with their pros and cons. For me, the N3 (currently) covers my "must haves" of big-screen and integrated business solutions (I was very worried at first that the stylus was just a fun gimmick that was pointless as a work tool. So glad I was wrong.)
The Nexus 5 has the plus of being "pure" Android with much faster updates direct from Google. Those are huge plusses in my book but not critical. They're not deal breakers for me. The tiny screen is, though. And, while it might sound appetizing to have a singular super-phone (I haven't truly heard this term get tossed around for almost two years), I think such a phone would be bogged down by trying to "please everybody" while excelling at nothing and we'd be left with fewer overall choices, which would not be good.
So, I'm happy with the N3....and I don't think if the N3 makes sense for you that a Nexus 5 would also...of course, if you can afford BOTH, then why wouldn't you? ;-)