This is my idea of how a system to improve equipment and weapons could work in Nin Online, without having a system to craft brand new equipment from scratch:
The first part to enhancing an item is discovering its quality. When you first purchase or earn a piece of clothing, accessory, or weapon (other than ninja tool) it should have a "???" for its quality. (With the exception of unique items like the 7 Legendary Swords of the Mist, Akatsuki Ring, and other similar items. These should automatically be classified as "Unique" in this system.)
There would be five different qualities possible for all items, with a sixth tier specifically for special items.
I: Common. This is the most basic tier, and no enhancement can be done on the item, consider this an item to throw away or sell.
II: Uncommon. This is the first tier in which can have Enhancement be done to it. This tier does not allow for Augmentation.
III: Rare. This is the first tier in which can have Enhancement and Augmentation. It may also be Enhanced twice.
IV: Exceptional. This tier can be Enhanced to the maximum of three and given Augmentation.
V: Legendary. This tier can be Enhanced to the maximum of three and can be given Augmentation. It also discovers a special effect such as increased stats, abnormal access to a Jutsu you don't know while wearing it, or otherwise.
VI: Unique. This is reserved for special items like Akatsuki Ring. Exactly the same to Legendary quality, but the special effect is unique to the equipment in question and cannot be obtained otherwise.
When you have an item with "???" for quality, it must first be scrutinized by an NPC, similar to the Jutsu Scroll shop, in order to begin Enhancing or Augmenting the item. When you go to get the item scrutinized, you'll need to exchange an item as a fee. Using more of the item will increase the chances of a better quality forcefully.
Once your item has been scrutinized and is Uncommon or better, you can begin Enhancement.
Enhancing an item will increase its overall stats, which are selected by the player on Enhancement. Enhancing an item simply costs Ryo.
Rare, Exceptional, Legendary, and Unique items cannot have the same Enhancement twice at a time.
Multiples of the same Enhancement can, however, exist on different equipped items. (IE: You have a Hat with +5 Agility Enhancement and Shoes with +5 Agility Enhancement, so you have +10 in total from equipment towards your Agility.)
Examples of Enhancement effects:
Increase Agility by 5.
Increase Strength by 5.
Increase Chakra by 5.
Increase Fortitude by 5.
Increase Intelligence by 5.
Increase movement speed by 5%.
Reduce damage taken from Fire Jutsu by 2.5%.
Reduce damage taken from Ninja Tools by 2.5%.
This is done in similar fashion to Enhancement, but requires specific materials in order to be performed, and only one of the same Augmentation will work across all of your equipment.
Augmentations would be special, stronger buffs that you can apply to your equipment than Enhancement that could change your character in more dramatic ways.
Traditionally, they would buff a Jutsu's effectiveness or empower your basic attacks in some way, but shouldn't be limited to just that.
Examples of Augmentations:
Prepared [Jutsu Name] - Your [Jutsu Name] has a reduced cooldown timer by 5 seconds.
Empowered [Jutsu Name] - Your [Jutsu Name] has increased base damage by 10.
Hastened [Jutsu Name] - Your [Jutsu Name] takes half as long to cast.
Poisoned Blade - Your basic attacks with Swords apply Poison I.
Spirit of Youth - Your Taijutsu Techniques grant you 10% increased movespeed every time they successfully damage a target.
Flowing Water - Your Water Techniques cost 25% less Chakra while standing on water tiles.
Legendary quality items should have something special about them, determined immediately on them being scrutinized as a Legendary piece of equipment.
This could vary from anywhere of allowing the player equipped with such an item to use a jutsu technique they normally wouldn't qualify for, such as a Wind Taijutsu user being allowed to cast Fire Wall Technique because they have a special Legendary piece of equipment, to other equally powerful effects.
These special effects cannot be rerolled, and are set in stone about the piece of equipment in question, even if the items Augmentations and Enhancements are reset.
Similar to Augmentations, these effects do not stack on multiple equipment.
Examples of Legendary Effects:
Hidden Technique: [Jutsu Name] - You can use [Jutsu Name] even if you do not meet the requirements to use it; you also know it while equipped.
Limitless Supply - Your Ninja Tools are endless, using a ninja tool or casting a jutsu requiring that tool will not use up the ninja tool.
Medicinal Duplication - Your Medical Pills never run out, using a medical pill does not use up the pill.
Extreme Speed - You have 20% increased Agility at all times while this is equipped.
Extreme Strength - You have 20% increased Strength at all times while this is equipped.
Boundless Chakra - The first time you would run out of Chakra every 600 seconds, fully refill your Chakra.
Secret Technique: [Jutsu Name] - You can use the secret technique not known to other ninja, [Jutsu Name], while this is equipped. This would be a special jutsu only obtainable while wearing the corresponding Legendary, not linked to scrolls. Requiring the correct element may be required.
Aura of Complete and Absolute Supremacy - While wearing this piece of equipment, your bounty is increased by 10,000 Ryo, increasing by 10,000 for every 24 hours it has been worn. On death, this equipment drops and is sealed from being equipped for one week. Produces a special glimmering aura on the wearer that gets increasingly absurd looking for every 24 hours it has been worn. After being worn for an entire month, the item no longer drops on death. (Does not include inactive time while the player is logged off.)
Unique items effects are considered "Legendary Effects" and are treated as such, but are not in the "Legendary" pool of effects.
This would be a special function you can do for the cost of a large sum of Ryo to reset all special qualities about an item from Enhancement and Augmentation, allowing new choices to be made. This does not reset the quality of the item, nor does it remove Unique or Legendary effects from an item. Once an item's quality is discovered, it is permanently that quality and will never change.
Once an item has been Enhanced or Augmented, it is bound to you. Using an Equipment Reset will unbind the item, allowing it to be traded and sold once again.
This suggestion would need at least one new NPC in every village/town to be the one you interact with for all of these effects.