I've played with Ars Magica a bit in a test world, and I would have to say that it doesn't really compliment the tech based mods. Pairing it with MFR or soul shards is just ripe for abuse. Now if it were on its own, or with carefully selected mods, it would be a pretty neat combo. Just with a cursory look over it, I can see some pretty major power loops not to mention infinite item generation. I did see a thaumcraft based mod (thaumic tinkerer) which allows for item duplication using thaumcraft, but you have to provide the aspects necessary, plus with the limited supply of vis (without a major setup), it is self-limiting in what you can duplicate.
Ars Magica is a direct magic use mod, where thaumcraft is indirect. So I could see these being paired together in a world. From my cursory overview of Ars Magic, the two don't have a lot of overlap at the moment. I understand the need for a Magic World 2. Having played Magic World 1 for a bit, if I were including Ars Magica, there are a lot of other tech based mods that I would have to consider not including. TE, Railcraft, Forestry... I'm not saying I wouldn't include these, just that a good hard look would have to be taken to see if they compliment each other or provide too many cross-mod exploits. I played magic world 1 for quite a while before even getting involved with Thaumcraft, and that was the main magical mod.
As far as the world gen goes, I've come across way too many abandoned mage huts. I found 3 within a 50 block radius. Now if there were underground ones and the above ground ones were pared way back, it would be less of an issue. I understand that these houses are the source of new spells, and on a big server, you would need a lot of them for everyone's use, I think there are better ways to generate them for SMP play that don't spam them across the overworld.