One thing that can be learnt from the Silver Ladder in Mage: The Awakening and the Lodge of Sorceresses in The Witcher franchise is that mages and politics are a fun combination. I think that the Synod and College of Whispers have potential here. Here's what I've thought of them:
The Synod
The Synod consider themselves to be the true successors of the Mages Guild, but wish to avoid making the mistakes of the latter. In their eyes, the guild became aloof from the concerns of the society it served. It enlightened its members and offered knowledge to the public, but didn't do enough for the common man. And recklessly loose regulation allowed the hubris of a few to cause devastation to many.
It has gained mass popularity by offering affordable healthcare and tuition (including teaching peasants to heal themselves) and by protecting people from rogue wizards and daedra. And they don't just teach magic. They educate mages, battlemages, healers, priests, historians, lawyers, politicians, the rich, the poor and so on.
The College of Whispers
The College of Whispers consider themselves to be the true successors of the Mages Guild, but wish to avoid making the mistakes of the latter. In their eyes, the guild became distracted from its pursuit of knowledge by getting mired in politics and red tape and by attempting to appease a populace that couldn't be pleased. Their ethos is very much like that of the College of Winterhold: members can study what they want so long as it doesn't bring harm to other members or the institution itself and while sharing knowledge is encouraged and rewarded, it isn't mandatory.
However, they hypocritically turn to politics for two reasons. The first is that they want a continent wide network to research and share knowledge between all known cultures and operating this widely safely requires the permission of governments and local rulers. The second is that the Synod is constantly attacking their organisation and so those who wish for it to prosper legitimately are forced to fight fire with fire.
Reception in Tamriel
Cyrodiil
Both are ubiquitous. The Synod maintains most of the old guildhalls, while the College of Whispers operates more discreetly in private properties under patronage of wealthy members and sympathisers (who can regular call in favours in turn). While the Synod has managed to claim the Arcane University as its headquarters, its heartland is Colovia. Whereas in Nibenese high society, open support for the College of Whispers is progressive and fashionable.
High Rock
Similar to Cyrodiil, but closer to a 50:50 split of favour between the two. The College keeps laboratories in remote parts of the countryside for some of its most controversial research. The various witch covens are a problem for the Synod. In practice, they don't directly confront more benign non-daedra worshiping coven such as the Beldama Wyrd and even respect some of their principles, but they what they can to draw away would be witches. They fight against the more antisocial covens and teach knights and witchhunters to do so more effectively. Whereas the College woos covens and its advocates are often apologists for them and Reachmen.
Hammerfell
The Synod is more popular in Forebear cities than the Mages Guild ever was. Crowns consider it to be subversive. The College of Whispers has virtually no open support, but it's there underground.
Skyrim
The Synod is seen as over bearing and Talos worshipers particularly despise it for not only abandoning him, but leading the way in his removal from Imperial orthodoxy. The College of Whispers represents the worst stereotypes of mages to them and has no more popularity. As such, most aspiring mages turn to traditional court wizards or the College of Winterhold instead.
Aldmeri Dominion
For diplomatic reasons since the White Gold Concordat, the Synod is allowed a token presence. The College of Whispers is given equal treatment, which is more than what they have Cyrodiil. This is because the Thalmor want both organisations in plain sight and both to be equally strong; as they fight against each other, they remain equally insignificant.
Morrowind and Black Marsh
Here, the Synod has virtually no cultural footholds and is distrusted by the authorities. The College of Whispers has made some in-roads with its cultural neutrality, but is mostly dependent on friendly native movements. For example, some young Telvanni are interested in working with them. They're the ones couldn't get an apprenticeship with a wizard-lord, but then most aspiring Telvanni fall into that category.
I could see that in Elsweyr, but in a more calm, cosy and genial style. More cushions, tea and cakes before the claws and throwing knives come into play.