My simple answer is this:

Use Unity for commercial games that you don't need too much flexibility with, or just for fun and the joy of making games (and not game engines).

Use C++ if you are making a game that is 100% flexible to it's core (and moddable ), and are trying to major in software development and want the experience (what better way to learn software development then to make game engines from scratch? It's like almost the hardest thing you could ever do. It would look good on your resume).

Or put another way...

Use Unity when your game follows pretty conventional game mechanics (like Unity3D is good for making quick and dirty FPS games) and you wish to rush and make a quick buck.

Use C++ (well, you can use any language that has a graphics and sound library readily available) when you want to do something that cant easily be done with conventional easy-bake-oven technology. (Most of these unique ideas eventually trickle down into the readily available engines)

Also, remember, Unity is not the only show in town. There are approximately over 9000 game engines for sale these days.

I've hypothesized that you can make more money selling game engines to developers than selling games to gamers- but both markets have become saturated.

I do like the Unity store though. Typically I export these assets and use them outside of Unity.