These thoughts are somewhat disorganized.

Mordor should add a complex and intricate crafting system.

To be of any worth the item system will probably need a serious revamp to accommodate any significant changes.

Players should be able to customize standard, quest and randomized equipment.

Standard mud equipment should be usable and considered the base level of power.

Alliance and Quest equipment should be considered tier 2 equipment.

Craftable equipment should be considered tier 3 but be difficult to obtain all the parts.

Random equipment should range from tier 1 to tier 3.

Random equipment should be obtained in a few ways:
Random drops from a mob, bonus drop from difficult-mprog mobs, craftable versions and be available for purchase as a quest prize.

The specifics of what stats would be randomized can vary but the points to determine stats should be vary greatly between the tiers.

In addition, some random equipment should receive negative stats to gain extra points to get bonus stats. But these bonus points should be halved.

All equipment should have a few upgrade slots. Once a particular upgrade slot is used up it can not be removed.

Craftable versions of randomized items could require three or more parts to make. For example, a bladed weapon would require a blade, a hilt and a pommel and once combined the stats would be randomized. Craftable items would have a minimum and maximum level range and if the character crafting is within the range the item is crafted at that level.

There could be a skill system involved with crafting and upgrading.

Just some thoughts.

Seems very similar to World of Warcraft, perhaps there is a way we can make it our own flavour?