One thing I'd love to see in game is the ability to upgrade raid loot using collectibles and/or other ingredients to keep them useful. This would increase the number of alternative gear configurations and keep old raids worth running for more than just a couple of items.
Some example upgrades:
Torc of Prince Raiyum: Wizardry III, Greater Spell Penetration VI -> Wizardry VI, Greater Spell Penetration VII
Battle Coin: Competence To-Hit +1 -> Competence To-Hit +3
Jungle Cloak: Hide +10 -> Hide +15
Rattle Charm: Greater Acid Lore, Greater Sonic Lore -> Greater Arcane Lore
Visor of Concentration: Concentration +10 -> Concentration +15
Staff of Arcane Power: Add Spells
Shining Crest of St. Marcus: Improved Devotion VI, Lesser Healing Lore -> Superior Devotion VI, Greater Healing Lore
Kundarak Delving Goggles: Spot +10, Disable Device +10 -> Spot +15, Disable Device +15
These could be done in several stages (ie. Wizardry III to Wizardry IV with one upgrade) with increasing costs.