I'm at work right now, so I don't have access to my game. But I have a question about the Mage Armor perk in the Alteration tree. The one where it makes stoneflesh etc. twice as effective if you're not wearing any armor. The question I have is if you are wearing boots or gauntlets will this negate the benefits of this perk? Or does it only apply to chest armor?

It applies to any armor, regardless of which piece, be it helm, gloves, or boots. One of the best mage helmets in game is light armor. This is why I don't go down that line.

well that seems pretty dumb. Do they even make gauntlets or boots for mages?

You need to wear cloth. But only if you actually want that perk. Other than that, there's no reason not to wear heavy or light armor. There are cloth piece a plenty except for gloves Those can be rare...

hmmm mage in armor, never really thought about that. looks like the points I put into alteration are wasted!

If you havent gone too far in getting the 30% magic resist is sweet

Items thats didn't have armor rating considered as clothing so not interfere with perk.
There is some gloves and hoods in game, I still didn't found shoes perhaps I was unlucky but I believe we can mod them into game since body slot for headgear legs and arms already in game.