As a frequent visitor to Malta I am quite amazed at the tacit assumption that the structures at, for example, Mnajdra and Ħaġar Qim are temples. I feel it is very much a "King's Suit of Clothes" syndrome: no one wants to stick out their neck and say that this is merely conjecture.
I would have thought that the logical assumption would be that they are communal dwelling places, or even an early castle. What was the first thing the Normans built on arrival? Not a church, but a castle. For any peoples, landing on a strange shore, the first thing would be to build a permanent dwelling, suitable for repelling any invasion.
If they are temples, it would be illogical to have two in such close proximity but if one regards them as fortified dwellings, it would be logical to have one close to the shore, and one on a nearby high point, overlooking the surrounding countryside. If you were building an astronomical clock structure, there would be no need to go through the trouble of roofing it over: it is unlikely Stonehenge ever had a roof!
It is time that we gave these primitive people some credence of sense, rather than blindly rushing to building a temple to some hypothetical entity, to build a structure essential to their survival from other peoples, and the weather.