For some reason, Mage Armor requires you to wear clothes.

This is not how the spell works in PnP, or normal NWN. I'd suggest changing this in EfU.

It really makes no sense, my wizard can't be naked and cast the spell? Its suppose to "CONJURE" armor around you, which is why it is a conjuration spell not a spell to "ENCHANT" something you already have.

Specifically, I dislike this because I can't use Mage Armor on my familiar. So if I do send it out to spy, it can't have protections on it from this spell which should affect it.

I think this is to get around the bug where it was stacking with armor.

We have indeed suffered through a bajillion bugs with this spell. It is so incredibly problematic. :/

It... conjures augmentations for existing armor (so that the target has a total of 4 Armor AC).

There is yet another way to implement it, but I'm not sure how much the exploitation detection will add to our lag.

I will, however, add to my to-do list the ability to cast it on NPCs that don't have armor, but it isn't a high priority.

Was the exploitation of the spell so rampant that the switch had to be made in the first place? (naked vs. clothed)

I had to fix Mage Armor in response to active exploitation, yes. Part of preventing it from continuing to be exploited involved making it a temporary bonus to the currently equipped armor. There is an alternative solution, but it might impact server performance.

Could you just give summoned beasties shirts?

No server impact, and the beasties won't even look like they have shirts on.

But all of the shirts would have to read:

I'm with stupid -------->

I said I'll have Mage Armor work like it used to on NPCs, since NPCs (especially ones without armor) are incapable of exploiting Mage Armor. It's also easier than equipping them all with shirts...