I was thinking over some general ideas about how the different magic using classes approach their spellcraft, and how it fits into the Five Faceted Faith. None of this has any real impact on game play, it's just a little in character flavor to make the characters something more than a checklist of available spells.
The only optional "rule" I'd consider in regard to all of this is maybe requiring an INT/WIS check (whichever is applicable) for one type of arcane or divine caster to learn spells from a caster of a different type. Arcane casters cannot learn Divine spells at all, and vice versa, but making the subtle differences in how magic users, elves and wiccas approach magic, for example, come into play with a fairly easy ability check once in a while might make the setting a little more interesting.
Arcane Caster Types
Magic Users - Whether they actively participate in the "religion" of the sphere or not, most magic users relate to the sphere of thought closely. Their approach to magic is an esoteric mix of math, science, allegory and symbolism, and obscure knowledge that allows them to start to understand how the multiverse operates. By subtly manipulating aspects of all five of the spheres, they begin to be able to cause real changes in reality that manifest as spells. Though some of their rituals may resemble religious ceremony or dogma, there is really nothing spiritual or divine about how a magic user invokes her magic.
Elves (and creatures like dragons with innate spell casting talents) - Some creatures are literally born magical, the balance of the five spheres that results in mundane life is slightly tweaked in one way or another in these creatures, sometimes giving them the ability to use spell like powers without having to learn, memorize, or cast them in a normal fashion. Elves are a special case, existing on a figurative border between the real, balanced realm of the Known World and the mysterious and magical world of Faerie. While elves are blessed with an innate magic that aids them in quickly understanding how to use spells, they still have to learn those magics like humans do. Elven magical lore is not quite as technical or mathematical as that of humans, and borrows some concepts that seem to derive from druids or shamans.
Wiccas - Wiccas tend to hail from cultures and societies that are a little more primitive, relatively speaking, than the human standard. Rather than science and mathematics forming a strong part of their approach to magic, they focus much more on the symbolism, allegory and simple practical application of magic. Proper magic users claim that this simple, undisciplined approach is why wiccas are incapable of mastering the advanced, high powered magic that high level wizards can, but most wiccas would respond that such magics are frivilous and not worth the effort anyway.
One quick note about the use of the term Wicca. For whatever reason, this is the term the Classic D&D designers of the 1980s chose to assign to hedge mages, tribal wizards and other "minor" users of arcane magic. In the context of the D&D rules and the Mystara setting, absolutely no connection to the religion philosophy of the same name in the real world is implied or intended.
Divine Caster Types
Clerics - While most clerics have at least a rudimentary understanding and acceptance of the Five Faceted Faith, they choose a unique way of invoking magic from it. Rather than learn to influence things themselves, clerics form a pact of sorts with a being or beings of Immortal existence, in which their devotion and service to the agenda of those beings is rewarded with the ability to channel a small portion of the divine power of their patrons. Some clerics are narrowly focused and only directly serve one Immortal, or a small selection of allied Immortals, while others serve the will of all the Immortals of one sphere, or those of all spheres equally, but there is no difference in the manifestation of clerical powers which of these paths they choose.
Druids - Druids view nature and reality as a delicate balance of all five spheres, and through this understanding, they learn to subtly tweak that balance in order to invoke their magic. Most druids are careful never to push things too far and upset the natural order, and will often spend time in meditation and contemplation before acting to avoid any unwanted side effects.
Shamans - Shamanic magic is similar to that of clerics, in that their power derives from other entities. Rather than distant Immortals, however, shamans look to the natural spirits around them; dead ancestors, the essence of living and non-living natural things, and so on. Also, rather than channel the power of these spirits directly, as clerics do, the shaman's service to the spirits is rewarded by the spirits basically creating magical effects for them. Clerics claim that the inferiority of these spirits to true Immortals is the reason for the somewhat weaker nature of shamanic magic, but most shamans and the spirits they serve find this attitude pretty insulting.