So since starting this thread (with amazing legs! thank you everyone! let's keep the great discussion going!), I've ended up storytelling. I'm an experienced RPGer, but am still generally a newb to Ars Magica, so it's been interesting to sort of see what sticks out.
Complexity in the magic system has been a non-issue. Everyone is very invested in their magi, and so a lot of the labor of things is done by players.
The complexity of all the source-books can be overwhelming. There's a rule for everything -- if you can find it.
I end up distilling a lot of complexity down into single, story-driven rolls. This probably reflects my experience (and enjoyment of) PBTA games...I basically find what skill(s) make sense, and do a PBTA style resolution.
Given the above two, despite having read thousands of pages of ars magica text, a lot of it...ends up getting tossed out and distilled into much simpler rolls. Why? Because managing all of that complexity if you don't have a ton of experience and mastery of the rules and the various subsystems is really rough. If I wanted to do it 100% by the books, it would take a ton of time, and lots of spreadsheets. I actually like spreadsheets, but I think that the complexity should really be focused on where it matters: magi and the covenant.
I don't really like 1d10 and the powerful/failure curve on abilities.
Professions are weird.
The skill system is not great.
I get the point and function of story flaws, but don't like them. With a lot of players, all who generally take them, I think it's a big burden on the GM to have to juggle all of these story flaws...and on top of that, players use it to offset things that make them powerful. Starting with a dog gives you a point? And then what...I'm supposed to turn the dog into a story? That might cost the player time? I dunno, I mean, I am all about PC-driven stories, about twisting the knife, etc. I like the burning wheel's approach here a lot. I think story flaws are not a great approach.
I do not like the approach to the infernal.
I do not like the approach to the divine.
I think Faerie is fine if you blur the lines a little and give them a little more agency than the rules imply.
I feel more strongly than ever that a game that maintains the spirit of "sorcerers and spreadsheets" but severely streamlines out literally everything else would be great. I still want highly researched sourcebooks, but I don't want everything to be converted into another skill table, another skill, another profession, another labor point pool. I want the core mechanics to be flexible enough to handle everything people want to do, and more source material is more just about what to do with that, vs endless augmentations that are a nightmare to manage.
Oh and I love the setting, but I feel like the fact that it is so tied to history is really stressful for me. As time passes, I feel like I should be doing all of this research on what's going on in medieval europe so that like..important things happen? But that's just a massive burden to place on someone. I made a thread asking about good timelines for this reason...I feel like this could be its own sourcebook. It just goes decade by decade and calls out really important stuff that happened in various places, and how that could tie into things. I find this aspect of the game absolutely overwhelming and have no idea how to manage it.