Daggerfall/Morrowind item enchantment limits were a nice touch, but not quite what I was talking about with the "form and effect" modifiers. Enchantment limits require you to use a better base item if you want to apply a more powerful enchantment, but they still leave any given item equally suitable (or unsuitable) for any type of enchantment you might want to put on it. Form and effect modifiers are about making this item better for one enchantment while that item is better for a different enchantment. Given a wooden staff and a more valuable steel staff, the wooden staff would still be better for fire spells (because wood relates to fire) despite its lower value/quality. If you're making a Resist Poison amulet, you'd be much better off with a relatively cheap Silver Jade Necklace (silver purifies and jade is strongly associated with poisons) than with a very expensive Gold Diamond Necklace (neither gold nor diamonds are sympathetic to poison or protection).
In any case, though, this is all a pipe dream for now. We'll have to wait and see what's possible after the CS is out (and probably a couple releases of SKSE as well).
Interesting idea, implementation of such feature will require to have good detection to determine which material or type of item will be used to apply changes to enchanting output, how determine material for example?
For example, I use calculation based on parameters of item (armor\damage rating, weight and cost) to determine material quality it was require maximum value limits ( I use daedric as upper limit) to determine durability of item, http://www.tesnexus.com/downloads/file.php?id=28537 make such table of suggestive parameter for items in Oblivion, perhaps such system will be welcome in Skyrim to determine material quality and cost in such cases it also can has addition for material advantages and disadvantages for enchanting like your idea suggest perhaps as well can be returned certain http://www.uesp.net/wiki/Daggerfall:Enchanting_Items but such detection will require SKSE and good scripting, perhaps detecting of certain words in item description can be used also to determine type and material of item.
The limitations are not silly, there's a reason for it: Balance.
There is better ways balance then reducing number of equipment slots and forcing enchantment be usable on different items, hope new Enchanting system is open for edits enough.