After dealing with the Cleric, the Thief, and the Charmer, I thought I'd tackle the Magic-User next, since it's actually pretty easy to deal with in terms of variants. Plus, I have to think a bit more on the Fighter variants.
The Magic-User is easy because the name of the class tells us exactly what the class does (uses magic.) We don't really need to think much about the archetype itself. It's also easy to create variants: change the way magic is prepared or used, or what spells are available. But there are a couple caveats to this on the way I think it should be done versus the way it's been done in the past. I think the way spells are prepared and used should be a feature of the magic used, rather than the class using them. Thus, if you give Cleric spells to a White/Black Magician class, they would be indistinguishable from other magic-users as a class (same hit dice, same experience,) but they would have a hidden piety/taint score that would affect the use of white magic. Similarly, an Alchemist is just a magic-user who uses preparations instead of memorized spells. And when I get around to doing an Illusionist, the main difference would be in the way the spells works (they would all be charms and illusions and can be disbelieved, but would be more powerful than the equivalent "ordinary" illusion spells, and would have different casting methods.) Illusionists should otherwise just be treated as magic-users.
One consequence of this way of thinking is that we have to reconsider whether magic-users should be restricted to one spell list, or should be allowed to acquire spells from other lists. When I did the White Magician and Alchemist, I assumed the former, but I'm thinking now that your M-U sub-class should really only determine what kinds of spells you start with, not which ones you can acquire. Acquiring spells from outside your normal spell list might require unusual effort; additional training, or researching Read Magic, for example. There may be additional side effects: the GM would judge how pious or tainted an ordinary magic-user is before that character could cast White Magic, for example. But each spell list would work according to its own rules, regardless of the character's actual sub-class.
Edit: Jeff Rients has posted a replacement for the standard Druid class; he notes that he would not treat Druid spells as exclusive to the class.
Some previous sub-class designs included additional powers that weren't actually spells. In the case of trainable skills, these should just be based on background and not actually a part of the class. Other powers, though, could be handled by mixing classes. For example, a "fire mage" or other "class" with affinity for an element could be handled as a Cleric (fire) variant, able to command even ordinary fire as if it were a living being, mixed with an ordinary Magic-User who just happens to have a lot of fire-related spells. There's no need for a special Elementalist class mechanically, even though there may be a recognizable Elementalist profession within the setting.
There's one exception to the "keep the rules for using spells separated from the class" principle: inherent powers, such as psionics or superpowers. This, as I've suggested, is best handled by using the standard spell lists or specially-constructed lists that follow the standard spell level system, but changing the way these powers are acquired, prepared, and used. The variant archetype (the Psychic) would only have one power per two experience levels, maximum spell level equivalent equal to half experience level, rounding up in both instances, and would not be able to create "magic" items or have any special ability to use such; but in compensation for the more limited number of powers, the psychic would be able to use these powers in potentially unlimited ways, using some kind of point system or (my preference) a fatigue/exhaustion system.
I'm still fiddling with ways that new spell lists can be created, so I'll have to save that topic for later, perhaps much later.