To stop everyone from giving their heroes and armies swords of +fire/+lightning/+ice/+mystic/+drain/+infinitedoom I'd prefer to have multiple enchant weapons and armors to be relatively rare. Here are a few ideas to stop that:
A- Enchantment kits used on items have an increasing chance to fail based on the number of current enchantments.
If i use an enchantments kit on an item with no enchantments I am essentially guranteed that this enchantment will take hold. After that, the next enchant has an increasingly higher chance to fail and use the kit without applying the enchantment. To discourage rich players from still making swords with 10 enchants on them there could be a maximum limit and/or a chance that every enchantment failure could destroy the item to be enchanted.
Example chances for an enchant to take hold based on the number of current enchantments on the item.
0 1 2 3 4 5
99% 66% 33% 15% 5% 1%
*All of these chances could also go up or down based on the material of the item, power of enchantment, or technology/skill of enchanter. The maximum enchants allowed on an item could also be dependent on any of these things.
**To discourage save/load whoring of items, have each item have a random number seed saved with it so that loading and trying again will only produce the same results. You could easily extend this to predetermine all enchant attempts when the item is created (i.e. enchant trys number 3, 5, 6 ,9+ all are failures for this specific item).
With this system, a rich end game player would probably have their armies equipped with 1 or 2 enchant items, while their heroes might be the only ones to possess 4X weapons.
B- All items have a set number of enchantment points and enchantments take up a certain amount.
You can go for the easy thing here and say that each enchantment takes 1 point or give players and modders more flexibility by having some enchantments use more of these points than others. I think it would be beneficial to allow enchantment points to increase based on certain technolgies and by using rarer materials in item creation (i.e. the rare valorite ore produces items that can take 5x the enchantment of normal iron items). I fear that this idea would still have many players maxing out their item enchants though, which is why I prefer option A.
Material Ideas
A simple system where materials that are more damaging/protecting do more damage and can take more enchants would work, but I would prefer it to be more complex.
Simple
Copper +1dmg 1 enchant max
Iron +2dmg 2 enchants max
Valorite +3dmg 3 enchant max
In a complex system, magical affinity for enchantments would an entirely different trait than the base damage/protection and would allow for some strange and rare ore/material types.
Complex
Copper +1dmg 1 enchant max
Iron +2dmg 2 enchants max
Valorite +3dmg 3 enchant max
Illuminum +1dmg 4 enchant max
Mysterium -1 dmg 4 enchant max
Volcanic crystals +1 dmg 3 enchant max (+1 if contains a fire based enchantment)
**Enchantment maximum could easily be replaced or combined with a +/- modifier on the chance an enchantment would take.