Is there any advantage to using clothes instead instead of armour?
All the enchanting I've done seems to be identical regardless of whether I use cloth or proper armour.
If both can be enchanted the same what advantage is there to NOT having the extra protection?

there are a couple spell perks that require you to not be wearing armor. cant think which ones off the top of my head though.

Only thing I can think of is that the "advantage" to clothes is just that you like the way you look in them better. Most of the armor (especially heavy) is pretty ugly - particularly on fem toons. Even Elven light is not very attractive. The ancient nord stuff that what'shername wears is okay, but it's not really ideal. I actually prefer wearing the "tavern clothes" you get off the vampire in Morthal, enchanted to whatever depending on the toon....

Clothes have little to no weight, and there is an alteration spells allows you to get about 300 armor when not wearing armor if you have the Mage Armor perk.

But in order to make clothing as good as armour you need to drop perks into Alteration to raise your stoneflesh effectiveness.
It seems like being punished for wanting to use cloth.
Are there ANY effects that can only be used on cloth or work better on cloth?

You're going into combat wearing clothes. Why would you NOT be punished vs someone wearing full daedric armor?

No

Someone just pointed out to me that by dumping perks into Alteration you don't need to use them on Light or Heavy Armour.
So that is the difference. Not what you enchant but rather where you put your skill perks.

Not really. It's the same argument as light vs heavy armor. The trade off in protection is weighed against the movement impairment/inventory space the armor takes. However, it is worth noting that even though the dragon priest masks are classified as light or heavy armor, they do not conflict with perks like matching set or mage armor, where you are required to wear a certain type of armor for the bonus (I think at least. Seems that way from my game).

Cloth = no movement impairment at all (heavy = slower, more stamina drained w/ sprint), no armor noise when moving (don't need muffle to sneak), any look you want, and best of all the whole set won't weigh more than 5 lbs.

Uh.... well, you know.... in almost every "background was AD&D" sort of game out there - if you want to play a mage (or priest or warlock in some games like wow) you are clad in cloth. And cloth is certainly not now nor has it ever been a good "armor replacement". That's the downside to playing a caster-class. However, as a caster class, you should be doing enough damage with spells that your lack of hard armor and its benefits won't be a problem - since supposedly you will kill those half-dozen mobs before they get in range of your mage's rags.

If that's not what's happening to you, then maybe you need to rethink either your approach to this game, or the stuff you're wearing. I point out though - most any non-mage around level 5 can kill 3 or 4 mages without breaking a sweat....

yea the problem here is that, unless im mistaken, there are no penalties for casting in armor. no spell effectiveness lost and without a strength stat anyone from a puny mage to a musclebound barbarian can wear heavy armor since they cant put a stat limit on different armor. The only benefit from wearing no armor is if your using stoneskin and have that perk.

While there are perks to remove the weight and slower movement of armors, it takes a few perks, perks which could perhaps be better spent by a magic-focused character.

It's Elder Scrolls: play how you want. Heavy armored sorcerers have always been a staple of this series, but so have robe wearing wizards.

Short version: armor makes you move slower.

I wish they would have made clothing/ robes able to have better enchatments, if I remember right (and I may be wrong) that in marrowind more expensive items could hold better enchantments. So I wish they would have gone back to this. Making expensive robes the best enchanting options. It would balance armor vs robes better I think. Armor give better dr while robes have better enchantments. Makes sence right?

You CAN enchant clothing/robes.

I missed a word there, typing on the iPhone svcks. I was trying to say better enchantments.