er.. yeah, a lot of things can be achieved in 3D, but layered clothing without extensive modeling work? I don't think so. Sure, if you want it to look like crap and have the models clip all over the place or show gaps here and there, no problem... but if you want to make it look right...
Well for example Soul Calibur IV
http://www.youtube.com/watch?v=IMVbrSMTtWM
http://www.youtube.com/watch?v=CRxR_Op_fAo
http://www.youtube.com/watch?v=ZUtKKS09oj4
An example of such system, you can decide by self looks its like crap or not, but I don't see cliping and gaps but I see animated parts on clothing, so layering can be achieved in proper way, http://www.youtube.com/watch?v=jY2QWXk_NsU& but when modders receive such system as base number of unique armors will be expanded even more.
You are correct, it is because of clipping. If you look at Morrowind armors, they are basically the same mesh with different textures, unlike Oblivion armors which have distinctive meshes for each armor.
If you open up the base body in Blender, then open different armor sets on top of one another, you'll see all the clipping that occurs. It wouldn't be possible to achieve layers without creating complete body part meshes for each layered item.. you maybe could get away with pauldrons, but only using big pauldrons on the less bulkier cuirasses.
One "cheap" way to create the illusion of undergarments would be to re-texture the base body mesh with some sort of clothing texture.
Clipping occurs and with Oblivion equipment, so removing of slots does not fix it, also removing certain slots make some parts of armors looks like created out of rubber, adding some additional bones can fix such flaws, new skeleton for example similar to skeleton of Lich in Oblivion and has pauldrons bones so pauldrons will not flex with hands anymore, they are done out of metal after all not from rubber.
Also additional parts like bags, belts, straps, amulets etc can be added to base mesh so even just retextures of robes like was done in wrong way in Oblivion http://www.tesnexus.com/downloads/images/37594-2-1300216010.jpg (but having real unique items still better)
So at last layering of such additions will expand variability more.