In my time as an A320 trainer with both CPL and MPL cadets, my opinion is that the MPL cadets were most definately lacking in not only their manual flying ability, but their confidence to fly manually. Some other curious observations was the lack of basic ability to taxi the aircraft. A rather candid confession from one student on the way to the aircraft led to him telling of how limited the sim time was, necessitating the aircraft being positioned at the holding point ready to fly. The little things we take for granted like braking and overshooting the nosewheel on tight turns was left out. This was easily trained but it, and other areas led me to believe that the MPL was not a complete package. (the process, NOT the students).
As good as modern sims are, I don't believe that they were ever designed for "learn to fly" type of use. There is more to learn in light aircraft than just flying around. Many of the MPL cadets didn't quite have a firm grasp on the realities of some situations. The rain repellent button doesn't freeze real life, it just squirts stuff on the screen.
The old fashioned CPL has served generations of pilots well and while there obviously are outliers at either end of the curve, a solid consolidation of the basics is essential. Is the MPL the way of the future? In my opinion NO, but there must be a better way to find a middle ground. The good parts of the MPL could be used as a faster step to full ATPL rather than bypassing so much of the old fashioned CPL flying.
Of course, every course is only as good as the individual on it. And indeed the company employing it. If it is used as a tool to get the shiny jet job and wear cool sunnies and take selfies in the cockpit at an airline that is using to fast-track cadets as it's too cheap to employ experience, then it's doomed to fail. If it is seen as a different pathway with it's own limitations and failings and a supplimentary method to crew the airline, then there could be a future. But I do think it needs work. You cant build a house from the roof down.