I just now got enough smithing to make glass armor, and I also changed followers from Aela to J'zargo. Im thinking of making some enchanted armor for him but not sure if magicka reduction would help him or not. Do caster followers run low on mana, or would he be better off with some other enchantments?

I usually at least give them a ring and a neck with resists. Magic resists all schools, but you get less overall resistance but it sure covers alot. I have noticed with mine that some followers won't equip some items with the same exact enchant on them , like they're somehow trying to not let you stack anything. They use their resources just like you do , so yes they can run out. But followers are pretty good at adjusting weapons spells etc. to an extent , I.E. I gave Mjoll the Lioness a staff and she equipped it and used it along with grimsever. So just experiment with stuff I generally enchant alot of defensive stufflike health and fortify(armor type) , and the rest with what you generally find on enemy casters like a master robe of destuction on a radnom mage for example.

I gave Onmund a set of Master Robes of Destruction, but he'll have none of that. He seems to think the Novice Robes of Destruction he came with are better. But if I give him armor, he puts it on. This (along with some testing of other followers) leads me to believe that when it comes to armor, they will always prefer to wear whatever has a higher armor rating. They don't seem to be able to distinguish between different types of robes (all with armor rating of 0).

To expand on this, they prefer to wear whatever has the higher armor rating for them. Many followers have different skill levels in different types of armor, so just because a piece of armor has a higher rating for you doesn't mean it will for them. For example, most housecarls will prefer heavy armor because they have a higher skill level in heavy than light, but using fortify gear + potions, you can get them wearing some upgraded Forsworn gear. The key is to get the armor rating high enough for their skill level.

Also, they will utilize enchantments, but don't factor them in when deciding what to equip.

Yeah, but for mage followers this does weird things. They don't have any armor skills to speak of, so generally they put on whatever has the highest base armor rating out of their inventory (but this did allow me to turn Onmund into a deranged Megaman by giving him Dwarven boots, gauntlets, and helmet, with the Shrouded Armor). I really wish they'd consider enchantment strength, though, because I'd like to give them better robes and have them actually wear them.

So far as I know, and have been able to determine, NPC's have an unlimited Mana pool. I have NEVER seen a caster run out anyway......

I use Erandur and he definitely does. If I don't give him a backup weapon he'll run up and start punching the mob once he's out of magicka. After giving him a lot of gear that boosts it it hasn't been as much of a problem, and I gave him a mace just in case.

As for weapons, they tend to use whichever weapon does the most damage before tempering or enchants are considered. For example, a Epic-grade Elven Sword does much more damage than an unimproved Ebony Sword, but a follower will use the Ebony over the Elven. And as said before, they don't consider enchants when choosing what to equip.