Background: I'm a computer-nerd, but since Treos and my first HTC G1, I have not been a phone nerd in years, just a semi-power-user.
My Android phones have been G1, S2, S5, Xperia X Performance. I've frequently borrowed and used various Nexuses/Nexi though.
Verdict:
I love Samsung base apps (messages, phone, etc). I've used Nexus, and now have Xperia [don't ask why], and I miss a million little things about Samsung. Changing font sizes in messages, integration between contacts & phone & logs, the design & usability. Can provide examples and details if interested - all of them are LITTLE things, but make my hourly life easier.
I do not in general use their "bigger" apps - with eventual exception of Fitness/health app, which I found pretty nifty.
I also repeatedly find that I prefer Samsung quick-bar to Google's Quick Bar, as absolutely hate Google's Wi-Fi button and selection.
Oh, and the fact I cannot have a simple button on home screen to start USB Tethering is driving me crazy (trivial on Samsung).