New stacking behaviors, as per http://www.gamesas.com/index.php?/topic/1110827-relz-oblivion-magic-extender-v1beta4/page__view__findpost__p__16323317, are scheduled to be implemented in v2.
That still doesn't address the single-spell case, though. The problem is that if the ResistMagic AV (which is also the weakness AV) applies to all spells, and if resistances apply before the stacking calculation is performed (which they should for various other reasons), then Weakness to Magic will always amplify itself. The new incoming effect, even if it's from the same spell, is modified by the target's ResistMagic which was increased by the previous cast. Granted, with the changes discussed above plus AVUncapper, this isn't as cheaply and easily exploited as it used to be -- but I'm fairly sure that making it completely unexploitable will require weakening it below the threshold of usefulness. Then again, I haven't yet put everything on the same page and checked the numbers, and if you have, I'll trust that for now! :goodjob:
I've been thinking through the consequences of various mechanical tweaks over the past couple of days and the only one I've come up with that doesn't annoy me somewhere along the line is a per-MGEF "item type resistance does not apply" flag -- preferably separate flags per item type, just in case. From both this conversation and earlier ones I get the feeling that's a very tall order, but I may as well float the idea to be sure. (Of course this could be even more complicated if Spell Reflection and Absorption are handled by the same code as Resist Magic and Poison. Not sure on that.)
I might have a better idea, though. Request, from Scruggs, a new function script hook that fires once for each loaded form that matches a particular filter (e.g. all spells, or all references to a particular base form). This will allow you to make sweeping changes of the form "give all X the property Y" without compatibility issues or new mechanics.
Hmm... interesting idea. At the moment I'm using a much simpler solution -- set all premade spells to explode in the CS, and edit new spells on the player as they're added/created. On the one hand, the requested GMST would turn "one script" into "no script" and that satisfies my instincts about minimizing the amount of code I have to personally maintain. On the other hand, that hook would be pretty damn useful for a lot of things. Decisions, decisions...

I think what you suggested is the most straightforward suggestion. Scripts on AV Tokens don't run constantly, they run once each time the value of the AV is computed.
Huh. "AV Tokens" sounds like I need to go read the docs... since AVUncapper got split out, I haven't really been following AddActorValues.