One flexible simulationist approach to magic was West End's Torg. This game had the distinction that the magic rules were internal to the game world; past characters had researched them (and research was ongoing) so the mages were aware of the magic rules. Researching new spells had clear mechanics, and getting good spells needed either a lot of skill or a lot of time invested, or both.
Also, Torg was a cross-genre-warfare system intended to integrate magic into the modern world. (Along with dinosaurs, horrors and cyberpunk, but you could just not use those rules.)
Torg's system encourages a cinematic approach with larger-than-life stunts - in some ways it's a moral precursor to Feng Shui.
What Torg doesn't have is a good research mechanic for anything other than new spells, and its large-group combat mechanics are simplistic. (We merged it with a wargame once for a campaign-end battle, however, to good effect.)
Torg books are a little hard to find these days; it's been out of print for a while. Key Torg books for the magic design system are the main book and the sourcebook for Aysle (Torg's magical realm). The spellbook, Pixaud's Practical Grimoire, is not crucial but has a lot of examples.
