The Oblivion mods http://www.tesnexus.com/downloads/file.php?id=16219 and http://www.tesnexus.com/downloads/file.php?id=25224 really inspired me to think on their possible application to Enchanting in Skyrim. I would fully recommend either or both of these to anyone who enjoys playing an even remotely Magic-based character and these are extremely fun mods for Spellswords, Battlemages, Sorcerors, Crusaders, Nightblades, and other classes with both magical and combat ability. First, I'll give a bit of summary on these:
Weapon Magic is a mod that adds new spells for each spell effect that act as temporary weapon enchantments. These enchantments can be cast on any weapon and have three enchantment ranges for each effect. The first is a simple On Strike enchantment cast on the weapon before or during combat that will activate the spell effect a single time against the first enemy hit by the weapon. The next is a similarly On Strike effect, but affects an area around where the opponent is struck by the weapon, inflicting damage on multiple enemies by striking one enemy. The last is a sustained enchantment that once activated will apply the magic effect to the weapon on every strike, like in normal enchantments, but channels the user's magicka through the weapon instead of having a certain number of charges and requiring soul stones. There are damage effects of every type including Fire, Frost, Shock, Absorb Health, Demoralize, Frenzy, etc.
Conduit Magic is another enchantment mod that uses effects similar to the sustained enchantment of Weapon Magic by channeling the user's own magicka to power the weapon rather than charges. The spell effect used is your equipped spell and the temporary enchantment can be dispelled or or changed to a different spell by simply re-casting the enchantment spell or switching the current spell to be used.
In Skyrim, we have been told that spells will be equipped like weapons instead of treated as intangible abilities. This somewhat eliminates the ability to cast a single short-term On Strike enchantment a la Weapon Magic. I do think, however, that somewhat mid to high level of perks could be used to incorporate some of these temporary enchantments.
For example, one low to mid level perk could be the ability to disenchant a weapon or item, allowing it to be re-enchanted with a different effect. This perk wouldn't be terribly convinent for a Combat/Magic Specialist, but would provide a way to change damage types or effects with a bit of pre-skirmish preparation.
A more powerful perk could then be the ability to channel the user's own magicka through the weapon rather than using charges. This will help the character when your soul gems are limited and your weapon's charges are running down, but you still need the extra oomph provided by a powerful On Strike enchantment.
One last and even more powerful perk would be the ability to change the effect of a weapon on the fly, even during battle! Similar to Conduit Magic's system, whatever spell (likely offensive only) you set to your other hand when using a weapon and spell combination would become the new enchantment on your weapon. The limitations here not encountered with Conduit Magic are the inability to dual wield or attack without a spell in one hand and the fact that you would need to have a non-defensive or healing spell equipped to do this. This would also need the ability to be turned on or off at the player's discretion so it doesn't override the weapon's normal enchantment(s) when you don't want it to.
Again, these are just a few ideas, discuss if you wish or add ideas if you want. The third perk would likely require far more work than the previous two, as there are quite a few limitations to fully changing enchantments on the fly. Also, I do realize these will likely not be included, especially so close release, if Bethesda hasn't already incorporated them, but a mod could still be created or something similar could be DLC.
EDIT: Added Valvalis-Orion Uvius's suggestion of Morrowind style recharge over time with enchanting. In Morrowind, enchanted items would recharge over time depending on your character's Enchant skill, Intelligence, and Luck.