Thinking about system and gameplay, in my view one of the problems D&D faces is ambiguity over the relationship between clerics, druids and MUs.
The default world of 1e is much more humanocentric than 5e. But the creatures the PCs interact with in 1e are not representative. They’ll mostly encounter monsters, including the evil tribal humanoids with their inferior shamans/witch doctors. In the wider, mostly human, world there are MM nomads and tribespeople, druids and later on the Unearthed Arcana barbarian. They’re not quite as subpar as the tribal humanoids – the leader of a band of nomads can be a 10th level fighter, an encounter with tribesmen can include an 8th level cleric – but they are still subpar compared to the urban/cosmopolitan sphere.
You’re right that the cleric is weird because it’s become a synthesis of elements from Christianity and an imagined polytheism.
The magic-user/wizard wields natural magic, in the sense of control over the impersonal occult properties of the natural world. ("Natural" is here used in a much broader sense than D&D uses it to include magical forces.) Though the 4e witch subclass, which I didn’t know about, seems to be an exception to this. The MU/wizard is like a medieval scientist. Jack Vance’s The Dying Earth suggests that magic is now largely performed by rote, the underlying theory having been lost:
"In ages gone... a thousand spells were known to sorcery and the wizards effected their wills. Today, as Earth dies, a hundred spells remain to man's knowledge, and these have come to us through the ancient books"
"I am dissatisfied with the mindless accomplishments of the magicians, who have all their lore by rote."
But the 1e MU isn’t Vancian in this respect. Spell research (DMG pg 115) assumes both a library and a laboratory which implies not merely recovery of lost information but experimentation to discover new knowledge. MU training costs (DMG pg 86) include "equipment, books, experiments, etc."
This passage from James Frazer’s The Golden Bough could almost be describing the magic of the D&D MU/wizard (except that their faith is probably explicit):
Thus its fundamental conception is identical with that of modern science; underlying the whole system is a faith, implicit but real and firm, in the order and uniformity of nature. The magician does not doubt that the same causes will always produce the same effects, that the performance of the proper ceremony, accompanied by the appropriate spell, will inevitably be attended by the desired result, unless, indeed, his incantations should chance to be thwarted and foiled by the more potent charms of another sorcerer. He supplicates no higher power: he sues the favour of no fickle and wayward being: he abases himself before no awful deity.
Unlike the Frazer-ian magician, the D&D wizard's magic works and their understanding of theory is correct.
I agree that in terms of what the MU/wizard actually does there’s quite a bit of overlap with the druid. D&D has a lot of class overlap problems because of the way it was built up by accretion, drawing on many different sources along the way. This wasn’t an issue in 1974 OD&D because there were only three classes – fighting man, magic-user, cleric.
the "witch"/pagan role in the gameworld which, in part, is a way of looking at the rural aspects of religion and spirituality through the urban/cosmopolitan lens.
The Satanic witch is imo the rural service magician viewed through the early modern urban/cosmopolitan lens, while the current neo-pagan witch is the rural service magician viewed thru the modern urban/cosmopolitan lens.
The 5e warlock class represents the former. It’s a bit weird having a class that represents a group as viewed from the perspective of its enemies, albeit altered to be no longer evil. The OD&D Chaotic (evil) cleric – a sort of Satanist, anti-Christian, or Conan-esque Evil High Priest – is in one way less weird, because it was written by those enemies, but in another it's weirder because they're allowing it as a PC.
In a fantastic magical world like that of D&D there’s no reason for the rural to be inferior to the urban/cosmopolitan. Everyone could have access to equally potent magic and other powers. But there’s been a persistent association of “tribe”, “primitive”, low intelligence, evil alignment, superstition, idolatry, and inferior magic. This has gotten worse in 5e compared with 3e and 4e.
Strangely two of the most important sources for D&D – Conan and Tolkien (The Hobbit/LotR) – don’t present the rural world as inferior to the urban/cosmopolitan. Howard considers it superior. Tolkien is a bit more equivocal – Gondor is a positive example of the urban/cosmopolitan – but I think he’s opposed to modernity, particularly industrialisation. The Two Towers: "Saruman… set some of his precious machinery to work… up came fires and foul fumes: the vents and shafts all over the plain began to spout and belch. Several of the Ents got scorched and blistered. One of them… got caught in a spray of some liquid fire and burned like a torch: a horrible sight." Letter #75:
There is the tragedy and despair of all machinery laid bare... it attempts to actualize desire, and so to create power in this World; and that cannot really be done with any real satisfaction. Labour-saving machinery only creates endless and worse labour. And in addition to this fundamental disability of a creature, is added the Fall, which makes our devices not only fail of their desire but turn to new and horrible evil. So we come inevitably from Daedalus and Icarus to the Giant Bomber. It is not an advance in wisdom!
Tolkien seems to be set against all human power, no matter its source. Industrialisation is a bad thing because it has produced the greatest amount of power in human hands. He wouldn’t like the high level D&D MU/wizard!