That, of course, is exactly why the whole of pre-ArM5 canon was ditched with Fifth Edition.
Of course, ArM5 canon is now about as big as the whole of pre-ArM5 canon, so the benefit has rather waned.
Short response: You can't give Ars Magica a thoughtline, because it means telling a large part of the fanbase that they are playing the game wrong. You can have a thoughtline for a new game you are designing from scratch, but not for something that has grown organically over 25 years.
That's not fair. They were pilloried for paying artists but not writers, on the grounds that people actually bought the fanzine for the writing, not the art. You can disagree with this position, but it is reasonable. (They were initially criticised by someone under the mistaken impression that they paid themselves but not the writers, something that is even more reasonable, albeit mistaken.)
You get to write for Ars Magica. If that's not enough for you, you won't do it.
There is a genuine problem here. I can run an Open Call for Ars Magica, and not get enough submissions to fill the book. I have, in fact. It is accepted wisdom among publishers that, if you run an Open Call, you will be swamped by piles of badly-written crap, because everyone thinks that they can write. Roleplaying is supposed to be even worse, because everyone does write for their own game. So, why doesn't it apply to Ars Magica? I suspect it's because most people who are interested have read the books and decided that no, actually, they can't do that. They've tried, and it's harder than it looks.
Writing for Ars Magica really is harder than writing for any other RPG I've written for. To change that, however, you would have to throw away huge chunks of the game and dump much of the medieval background. I tried just throwing away all the previous canon with ArM5; it's not enough. Coming up with a thoughtline for ArM is one approach to throwing away huge chunks of the game. If you're going to do that, it's probably the best approach; you need a good reason for the swathes of destruction you're going to cut, and something solid to fall back on when the fans bay for your blood.
But if you're going to do that, wouldn't it be better to design a new game?
I'd say that my strategy on ArM5 has worked. The game has stayed commercially viable, and we've produced a lot of, in my opinion, excellent supplements. The only person who worked on ArM3 who has also worked on ArM5 is, I think, me. (John Nephew doesn't really count.) Thus, we have managed to almost completely refresh the author pool. I'm not, however, sure that Ars Magica, rather than a different game inspired by it, could ever have mass appeal.