This has crossed my mind too - a good way to use the game system for a gaming group that is not excited about a herd of magi, or even to slowly introduce the system to work up to magi.
Several points for consideration -
You could have one NPC mage, solo, as the "patron" of the group. Each PC would have been attracted/recruited because of something they offered, but each are rarely called upon individually. If an "angel"* is needed, the magus/maga is perfect, as the PC's wouldn't know the actual extent of their abilities. (More magi are possible, but with some explanation for why they are both distant and not overly-demanding of the PC's time.) This "wizard" could be of any power or background, from a failed apprentice or hedgemage who is not significant enough for The Order to recruit, to a lone Hermetic Archmage of incomprehensible potential. (This could even be of a Realm other than Magical.)
(* "angel" - a term in writing/scripting for a powerful character who usually stays offstage/offcamera, but who appears when "help" is required by the main characters. Often this takes the form of resources or key information, but can include anything that helps the plot up to a complete Deus ex Machina intervention such as a dramatic rescue or mysterious ability.)
Or, the NPC "in charge" could be a mundane who has connections to such - further removed and less expected when they show up.
You could have one PC be the default leader/authority - the lord/seneschal of the manor, the owner/manager of the merchant company, the autocrat of the library, whatever. (But the less independently capable, the more balanced the power focus). Also, that character would need a reason to go become involved, at whatever level your saga plotlines dictate (mundane characters can be the equiv of labrats too, potentially very dull.) Or, by having that "lord" be an NPC, you allow the players to be more self-determined.
The more "high fantasy" these institutions are, the easier it is to incorporate a wider range of character concepts, I would think. The higher the fantasy concepts for the central institution, the easier to tell a wide range of stories, tho' I don't know how your tastes run. Perhaps something that any PC mage would love to have as a contact - a library that pursues and collects arcane knowledge, perhaps a merchant who deals with covenants, buying and selling rare ingredients and magical dinguses, or (at the extreme) a private group of "exceptional mercenaries" who are known to be for hire for any mission impossible, for the right price.