Hi there!
Lurker here, and quite a long-time ES modder (I mostly modded Morrowind, being rather disgusted by Oblivion).
Here I've a smallish proof-of-concept mod I've made:
Multiple Ammo types for weapons
Being just a proof of concept, it's only for 10mm pistol, however it does illustrate how transparent for the player it can be made.
(From readme)
Once you equip the weapon from your inventory, it will simply equip the item if you only have normal rounds for it, will automatically switch for AP if you only have AP rounds, and will ask you if you want to load the gun with AP or normal rounds in case you have both.
Vice versa when you have 'Ap rounds loaded' version of the gun.
In the commends, there was a good idea about having multiple 'modes' for weapon this way, even w/o ammo types. For instance, switching between weapon and underbarrel GL, switching firing modes (auto/single), etc.
Still a hack, of course, but engine would simply not allow anything like that otherwise.
Of course, making AP rounds MATTER is an entirely different business - that the point of this tread.
But, enchantment idea, while good, does have it's drawbacks (thought about it myself, btw).
It would not allow for damage increases from skill... but question is, SHOULD there be increase of weapon damage from skills? It's not cannon, and it's not logical, too. Damage should come from accuracy and perks.
Next, what about critical strikes?
But I guess it could be worked around, too - just add appropriate weakness to damage type, 100% in case of 'normal' critical, and extra 20% with perks.
Kinda logical, if you ask me.
The alternative method would be to up the critical mult to 100%, and make damage PURELY scripted, via crit effects.
And with scripts, MUCH more can be done, including thresholds, colorful critical hits descriptions, instakills and whatnot. But it will involve much more work in the scripting department, and some things might not be possible (or vice versa - GECK is really greatly improved in comparison to CS, and there is script extender already available).