Debugging problems can get really hairy because of the two layer split, and it's just not worth it if one is running Marathon as the only framework.
I came to the conclusion that Mesos' biggest strength is giving people the option to write their own framework. It's not difficult, and gives you a lot of power over execution.
Marathon itself appears to be very simple, but has some really weird shortcomings. For instance, it's not possible to submit a deployment and then check whether everything went well, except if you manually compare the deployment before and after (this was still true as of 1.4.x).
Furthermore, Mesosphere abandoned the Marathon GUI, and I got no clue how the work of transitioning that part into the hands of volunteers are coming along, but this was essentially what tipped the scales for us.
(We're currently migrating from Mesos to K8s.)