Taking hints from Star Wars: The Old Republic and from Minecraft, I have an idea for an item modification system for almost every type of non-consumable gear. The goal is to make it easier to customize your gear to match your playstyle.
Here's how it would work: A new type of "Data Sample" item would be added, called Upgrade Modules. There would be one for every modifier suffix ([Dmg], [Pha], [Full], etc.) and would be obtained in two (maybe three) different ways: By crafting them at Memory Alpha or the Qo'nos Forge (Hereinafter "MA/QF"), by reverse engineering items, or (maybe) buying them on the exchange.
Upgrade Modules could take high amounts of Mk I (red) Data Samples to craft. This would allow players of any rank to craft them, with the high price to prevent them from being overpowered.
Reverse engineering would take place at a special Item Modification Console at MA/QF and would take an item of your choosing plus a sum of Dilithium increasing with the item rarity; and give you the Common quality version of that item and the respective Upgrade Modules.
Here's an example of reverse engineering: A player takes a Phaser Stun Pistol Mk VI [Dmg] [DoT3] and puts it through the process. Being a rare item, it would cost more Dilithium than an Uncommon item, but not as much as a Very Rare item. You would also need some research skill (Item Mk. * 100?) The process would yield three items: Phaser Stun Pistol Mk VI, Upgrade Module [Dmg], and Upgrade Module [DoT3].
Upgrade Modules would be used for Item Modification, which is basically reverse engineering... in reverse. You would go to the same console at MA/QF you use for Reverse Engineering. There, you would take a compatible item, Upgrade Modules, some research skill, and a decent sum of Dilithium (Dilithium cost increases with the rarity and rank of the item yielded) and out comes the item, upgraded with the respective suffixes of the Upgrade Modules.
Now, the limitations: Neither item modification nor reverse engineering will not work on any item that is not a non-device Ship Item or Personal Item. (Tetryon Particles, Terraforming Systems, and Tribbles are out.) Also, due to their specialized nature, it would not work on many (if any) Ship Consoles, Personal Kits, or special items (Jem'Hadar, Reman Prototype, Fleet Items, etc.) When upgrading, you could start with a Common, Uncommon, or Rare item; so long as the end result doesn't end with any more than three suffixes. (No more than three Upgrade Modules for Common, two for Uncommon, or one for Rare.) You can't upgrade an item with invalid Upgrade Modules, (putting [Acc] on a shield array, or both [W->E] and [A->S] on the same Warp Core, would not work,) though some Upgrade Modules could be put on multiple types of items. ([Dmg] could be installed on both Personal and Ship Weapons, [Cap] could be put on either a Personal or Ship Shield.) Dilithium costs could be adjusted to make it difficult to just pull a Very Rare Mk XI item out of thin air. Finally, a custom piece of equipment would bind to your character or account, to prevent players from making a fortune on the best possible equipment.
Thoughts? I've tried to be as cohesive as I can, but I'm not sure how well I did at that. If you need me to clarify anything, just let me know.