I got a flat top Ruger AR with flip up iron sights. I put a Vortex Strike Eagle 1 - 6 power scope on it. I wanted to leave the iron sights on as a backup, but could not find a way to do it. So I just left the rear iron sight off.
One big advantage I see in iron sights is that they are less likely to break. But because of the way the rear flip-up sight sticks up on the flat top it looks more susceptible to damage than the scope. And if you carry the rifle with the rear sight down it's just one more thing that will slow you down a little if you want to aim and fire a shot quickly.
I put a scope on another AR and put backup iron sights on it in the form of heavy duty sights that go on at a 45 degree angle; this makes it easy to transition from one to the other; all you have to do is cant your rife to use the irons. But that made the rifle effectively thicker and cumbersome so I sold it (there was something else I didn't like about the rifle too).
People who know the subject better than I do seem to be fine with a scope only and no backup sights. And I can see why. So I'm going to stay with one or the other, unless I find a good way to have both. Either way though, I don't like the flip-up sights I've seen, because of their prominence.