There's a lot more to it. I don't think the edges of the sword are equal.
Upgrade too early and some apps won't work correctly with the new software. There were some bumps to start with but that's expected. I think that most apps that are under active development have ironed out their Marshmallow bugs in the past 5 months. Are you guys talking about apps that have ceased development? I haven't run into any that completely fail on Marshmallow at this point (but I haven't tried them all). However, I know don't expect apps that modify core system behaviors (like Widget Locker) to work after the core system has changed so much since 2013 (Widget Locker's last update).
Stick with the compatible handset and it may take several months before you get the latest OS update. If you choose this route, you are putting those one or two apps over and above better security, major OS improvements (e.g. doze) and even fixes to broken OS features (e.g. LTE radio fix, do not disturb misbehavior, etc.). In the case of any phone vs. Neuxs, you're also accepting the fact that your phone will only get a couple of updates before it's abandoned and, as you said, those updates will take a long time to reach you.
In my opinion, keeping the compatible handset is on the much sharper edge of the sword.