Here we will discuss the difference between both deserts dunes & connectivity by roads.
If we talk about Zagora, then the Ennakhila small dunes, Mhamid Chigaga giant dunes, and Tinfou & Lihoudi medium deserts come to mind. Most tourists prefer to spend a night in Zagora Ennakhila because it is not far from Marrakech for trekking and hiking groups.
About Merzouga & Erg Chebbi dunes, it is not far from the national road of the province & most of the travellers can travel to the dunes. This accessibility is due to excellent roads connecting big dunes. Thus, making it easier to spend time here when travellers are running low on time during their vacation.
Suggestions for travelling to the Sahara in Morocco :
If you are looking for a trekking adventure, I suggest Erg Chegaga Sahara for a two-day trip. However, the Zagora & small dunes of Merzouga are suitable for a 3-day/4-day/5-day journey.
Moreover, you can also come across the Foum Zguid desert, Guelmim desert, and Dakhla desert. They have a different vibe than the South East of Morocco & all of these parts are closer to the beach for the summer holidays!