I will no doubt be coming back to this subject repeatedly, as it is the most difficult aspect of translating WRG Ancients and Medieval to a roleplaying context.
In the basic miniatures game, magic is treated very abstractly. Figures (specialized magicians, generals, or unit commanders) with magical powers are allowed to add or subtract the result of a standard six-sided die to the morale check roll of any unit within a certain distance (150 paces), but also not within a certain distance (100 paces) of opposing religious figures. (I'd house-ruled that magical powers also added 1-6 scouting points, but this was not a part of the rules as printed.)
This is not useful to me for roleplaying. What it does point out, though, is that magical powers should not replicate artillery. The magic of this roleplaying game should be more subtle. Happily for me, there are two magic systems that I can look to for a model, and they happen to be the two magic systems of which I am most fond. These are the system in RuneQuest and the "Path/Book Magic" system in GURPS Thaumatology (originally the "Ritual Magic" system in GURPS Voodoo, GURPS Old West 2nd edition, and GURPS Spirits). My current inclination is to develop a system that incorporates elements of both of these.
This means that a magician in this system will not be the "spike damage" specialist of current roleplaying, but will more resemble the "buff" specialist. Most magic will give targets bonuses or detriments to various abilities, perhaps, though some magical abilities will be more directly applicable. I've been analyzing medieval grimoires, folklore collections, and similar items to determine what people in the past believed they were capable of doing with magical powers. Unsurprisingly, many of these are targeted at mundane activities of limited use to adventurers, such as victory in court and the like, but others are very much of use, such as finding one's way or victory in wrestling. Other described magical operations, like invisibility or finding buried treasure (really!) are especially of interest to adventurers.
I'm still considering whether these should be discrete spells, like RuneQuest, or groups of abilities under a magical path like Path/Book Magic. I do think that some system of magic points will be important, since that gives us a resource management aspect. I may borrow an idea from Fantasy Wargaming, and require magicians to engage in stereotypical activities (studying arcane tomes, chanting, and the like) to regenerate magic points. I might even look to Unknown Armies for ideas on the subject.