Well currently I'm running a game set in 790. In one of the previous grand tribunals, I was up front with my players are about some of the politics. "if you do nothing, you will get the status quo in the rule book, if you do something, you can change history." They opted to change history.
As a blank slate for my own saga:
0.) Start the game with the assumption that the PCs are going to change the timeline - possibly dramatically
1.) I would change some of the limits of magic regarding time.
2.) I would get rid of house verdituis altogether, and have their virtues integrated in as part of hermetic magic.
3.) Merge Bjornear and Merineta - one faerie/shape changing/nature house is plenty.
4.) Jerbiton's focus would be on grand pieces of magical art - giant medieval epeen contests
5.) Trianoma and Guernicus would a single house dedicated to the stability of the Order
6.) Criamon would be a house of pagan mystics worshiping the old gods
7.) Flambeau would be the enforcers of the edicts by the new house mentioned in 5
8.) Tremere and Tytalus would be two rival political camps of the Order instead of actual houses. Many magi are part of neither camp. Both wish to dominate the order, but neither will let the other do it. The tremere wish to dominate by uniformity (magic academies, social engineering, meditation, peace) etc The Tytalus wish to dominate the order through direct conflict, passion, personal strength, and power - only the strong deserve to be members of the order.
If a magus can resist the Tytalus, then they are worthy otherwise, they are chaff to be separated from the wheat and discarded. Only though the efforts of the Tremere are the Tytalus thwarted. Yet at the same time, given the point (10) below, without the Tytalus the Order would be woefully under-prepared to face external enemies.
9.) House Mercere would be a group of magi who facilitate trade between the different houses as well as between magi and mundanes. Message carrying is just a bonus.
10.) Multiple rivals to the Order of Hermes - it simply cannot sit around and rest on its laurels. New hedge traditions appear out of the blue every few decades or so causing serious angst to existing covenants of the Order. Implacable viking raiders. Mysterious Persian and Arabian wizards leading raiding expeditions deep into europe for magical goodies. Roman wizards coming out of Regio's trying to rebuild the roman empire. A rival order, perhaps like the Augustan's, carefully bound into the status quo of europe - competition for Apprentices is fierce.
11.) A distorted historical timeline assuming the supernatural
12.) Combining Magic and Faerie into one.
13.) House Bonisagus is constantly pushing new boundaries of magic, a series of discoveries with chronological start points that over time will cascade together to have various effects on the game.
i.e. (961 - designer babies ala ancient magic. 1028 - alternative to longevity potions, a powerful ritual that lowers a magus's age, 1077 - break the limit of energy) etc that kind of thing.
14.) The setting more integrated with the Order - factions of the Catholic church actively working with Magi to do good works for the poor, crusading, or building cathedrals. A properly built magus with a few rooks of creo & terram vis can save the church decades and centuries of time and effort to build churches and cathedrals.
15.) All magi have the gentle gift - but can get the effects of the "normal" gift or blatant gift as flaws or through twilight/warping.