Yadda, yadda, make your own mind from random bits thrown by all of us.
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The Covenant is a character
That's the first consequence of Troupe-style, everyone should work together to build a stage where their stories will be told. The structure and the grogs are a common resource that everyone will play as support characters. Even neighbors and adversaries can be handled by players. -
The Alpha Story Guide is just a facilitator
Troupe style and Story Flaws implies that players have to take the lead. It's less adventures into the unknown and more theater and improv. Take for instance a Criamon who wants to do his next station, you should both roughly plan how the story will flow to allow the player to build his personna and make the choices that will bring about the consequences he's looking for. -
Charop and retcon
Designing magi is a much more involved process than in other games. Getting it right the first time and avoiding the traps is not easy, you should allow to revisit the concept and correct the character. Also, if you consider adventures as "retelling of a legend from 100 year ago", it explains the inconsistencies in the same way that Merlin's myth places him at different locations at the same time. -
Long term events
In some systems, getting a month of downtime is unusual. You would spend 4 sessions of play handling 36 hours of game time. In Ars Magica, 4 months of game time will pass by in an hour, a little 15 minute visit to the local noble followed by planning your next season in the lab. After all, your magus will be active for 100 years and more and 100 season-long sessions would cover 25 years in 2 years. -
Failure and consequences
You are supposed to fail, or at least not quite succeed the way you wanted. There will be consequences to your actions: nobles, church, faeries, tribunal politics, someone will not be happy that you solved a problem. You won't be gone to another adventure after 3 months so they will have 10 years to plan their revenge. -
This is a team effort
Sure you can drive the show, and if you're good enough your players might be happy to take the backseat. But just tracking the character's evolution is a lot of work for a single person, make sure everyone is involved in the effort. -
Middle Age and the alien mindset
Mythic Europe background is fully developped, just using wikipedia you could spend week reading on places and peoples. And there are many weirdness such as no inertia, spontaneous creation of maggots and poor's hour at the end of market days (anything unsold becomes free).
Also, see cj.23 simplified Ars Magica concept game, or how to play without character sheets.
https://forum.atlas-games.com/t/who-is-ars-magica-6es-audience/9640/121