Wow... a girl goes to a meeting for a few hours and the thread blows up! LOL
First of all, I made the blunder of uploading beta 2.0b2 without the scripts folder this weekend, so a few things weren't working (notably, players weren't getting the "dispel shield" spell and mage armor was not working correctly due to the missing scripts). I added the scripts to the zip and re-uploaded it before my meeting tonight, so if you downloaded beta 2.0b2 and do NOT have scripts, I apologize for the bugs. You can re-download now or wait until I get beta 2.0b3 up in the next day or two.
OK, question and answer time:
This could be balanced by leveling your alteration skill whenever you get hit with the shield in place. Similar to how the armors work. Nothing to drastic though. As for why your skill would go up in case people are curious? Maintaining the spell takes concentration and when under extreme duress(getting hit) you learn new ways to use it so your alteration skill goes up.
Already ahead of you. The mage armor script has a bit of code that gives you a little experience each time you get hit while the spell is active if you have the permanent version of the spell. The amount of experienced gained is based on your alteration skill level. The exact formula is: skill level * .7 - 20. Since you must be level 50 to get the perk, this results in 15 - 50 xp per hit, depending on skill level, which works out to about 100 hits to gain a level.
I'm using version 1.30 and have just realised that the 'mage armor' perks are not existent on the alteration perk tree. Where they usually are in vanilla, it is replaced with the 'less is more' perk. Is this right? Or should I not be seeing a mage armor perk somewhere on the alteration tree?
Also, am I ok to replace this old version with the new one without endangering my save game?
That is correct. In version 1.3 I tried building the Mage Armor directly into the flesh spells and offering some generic "be better at magic" perks instead. I wasn't very happy with that solution, so when I started rewriting the mod in the CK, I put the Mage Armor perks back in but changed their functionality (hopefully for the better!) And yes, you should be able to update without breaking your save.

WARDS WARDS WARDS
I spent last night and this morning implementing the new wards. Here's how they work:
- Wards instantly change up to your restoration level, meaning at level 20, you instantly have 20 ward power, and the other 20 will charge up over time.
- Wards are free to maintain (justified since you can't regen magicka while maintaining the ward) but drain magicka each time they are hit. The magicka amount drained is equal to ward power spent.
- Wards provide experience each time they successfully protect the caster. (Again, equal to ward power spent)
- The magnitude of the ward scales based on restoration skill if you have the novice perk (sort of a hallmark of this mod)
- Since the magnitude scales, you really only need the novice spell. As such, I've changed the name to "Ward of Protection" and am replacing the other wards with... other spells.

I'm also replacing other redundant spells like the more powerful versions of turn undead, repel undead, heal, and heal other. (These will also scale up in magnitude as you perk up the resotration tree) Be looking for cure poison, cure disease, resists, fortifications, etc. instead.
You could also add perks that, for example, create a blast centered around yourself that knocks enemies away when the ward shatters.
Hahaha, I love it!!!