Another change I'd make:

In Ars Magica (current edition) I'd fiddle with the way that spell penetration works. Currently, the penetration of the spell is based on how much you beat the spell difficulty by - which means that the less powerful the spell is, the greater penetration you can get on it. In the last ArsM campaign I played in, this led to the ludicrous situation of the PCs researching the most low-level demon-hurting spells they could get in order to exorcise demons, because they were having trouble getting a high enough penetration on their current  demon-zapping spells.

To my mind, this is precisely the reverse of what you want - if you're dealing with something with powerful magical protections, you should be busting out your most powerful magic. So I'd change it round such that the penetration was based on the number you roll (this will entail changing the numerical amount of spell protection people get out of Parma Magica and other forms of magical protection, but it'd be worth it), the effects of the spell depend on the difference between the dice roll and the spell difficulty (so if you only barely make the roll the spell doesn't do as much as if you ace it), and spells need to be a level of at least equal to half the required Penetration in order to have any effect at all.