I agree. The glow must go!
The best alternative, to my mind, is to simply create a unique mesh and/or textures for an enchanted version of any base item. This could include runes, glowing sigils, simple design and colour variations, or any combination of the above. Whether or not that's viable (time- and resource-wise) is probably a question only a game developer can answer accurately.
And considering Skyrim's graphical and technical improvements over Oblivion -- not to mention Morrowind -- even a generic "glow wrap" effect might look a good deal better, and more subtle, than it has previously. Less is more in this case, though, for sure.
Well create an unique mesh and texture is not simple task and definitely will strike down variability of items, developers mostly will ignore time consuming modeling work
More expected if there will be better shaders on enchanted items, developers already take steps in thats way in Oblivion and can improve it better like in this mods for example
Enchantment and Hit Shaders
http://tesnexus.com/downloads/file.php?id=22147
Visual_Enchantments
http://tesnexus.com/downloads/file.php?id=19396
Soolies Better Enchantment Effects
http://tesnexus.com/downloads/file.php?id=30489