An interesting idea, but seems to complicate what is otherwise an effective and simple solution. It still seems like a Master Alteration mage, would opt for either Expert or Master level spells, essentially making the lower tiers useless for stronger mages (as they currently are).
There are already magic resist (and absorb) perks in the Alteration tree, so those bases are covered. I would leave the armor timers alone, and simply add scaling elemental/poison resistances (or reflections) as the spells get stronger. Novice can have 1, Apprentice 2, Adept 3, Expert 4, and Master can both resist and reflect. OR, have each type resist all elemental/poison attacks, scaling up from Novice. (basically scaling up like armor level does).
The danger you run into by setting one type of resistance on one armor spell, is that the player *cannot* disspell themselves to put on a lower tier spell with a new resistance. And you don't want to lock yourself into only one resistance when there are several out there.
I also dislike the "boss armor spell" idea, since it essentially shortens something like Dragonhide back to <2 minutes, making it a spell you can only use when you *know* you have a tough fight coming. You can't run around with it on as your primary defensive spell, due to having to recast so often. Unless of course, you buff Ebonyflesh up enough to compensate.
And - any spell meant to last for a duration that isn't a damage spell or damage shield, is useless with a timer less than 2 minutes. A long time ago a MMO called Asheron's Call had super short buff spells - mages were constantly casting them over and over to keep them up, and it was a major hassle. There was no strategic reason to cut them so short, other than to annoy the characters and place them in unnecessary danger because their "shield suddenly dropped". That's about as fun as dealing with browser popups.
Compare to a warrior that perked half the smithing tree, and half the heavy armor tree (i.e. almost one complete tree). They get to stand around, 100% of the time, with 100% armor on for 80% effective full-time protection. If you perk most of the alteration tree you get a similar effect (in BM 1.3), but still have to recast and spend magicka on a regular basis. If you drop those timers even further, armor becomes a combat only consideration, and you will get jumped running around without armor on.
Less annoying, more reliable is my vote. If you want more "exciting" alteration defense, make elemental protection spells. Don't go and hack up the reliable armor spells we now have.
