So there's no way of taking their default armor while they're a follower? Then they'd have to wear the good stuff.
Well, that or they'd go around in their skivvies...
I played around with Rayya and Gregor. I've been able to give them, say, a pair of boots with a higher normal damage rating which they equip. If you pickpocket their base boots, when you leave and come back they're walking around barefoot.
So what I've done is pickpocket their base armor and enchant it (enchantments that work on followers: http://www.uesp.net/wiki/Skyrim:Followers). I give back their enchanted base armor and take back whatever I gave them in the first place. Seems to be pretty stable with no one walking around nekkid.
That doesn't help esthetically but my character feels better knowing they're equipped as best they can be.