Neither option is universally better — it depends on your tolerance for logistical friction, your budget priorities, and where in Morocco you are actually going. A fully independent trip works well for the coastal cities and the medinas, where buses, trains and cheap riads are plentiful. It gets harder — and occasionally genuinely frustrating — once you head for the desert, the high gorges, or the more remote Berber villages of the Atlas.
I have done Morocco both ways, and the honest answer is that the travellers I have met who were least enjoying themselves were almost always the ones trying to get a 10-hour CTM bus to Merzouga on a fixed return timeline, or navigating the Fes derbs alone after dark with a phone that had lost GPS signal inside the walls. The travellers having the best time were either fully committing to the independent slow-travel approach (weeks, not days) or combining guided logistics for the difficult bits with free time in the cities.
Below is the side-by-side breakdown, the real cost comparison, and a practical verdict for different traveller types.