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-Remove Need/Greed/Pass loot system. I know this sounds like a big change but the system has been used for a long time in MMO's at it's showing it's age. Bear with me while I explain. Instead, have drops be individual (instanced) for each player (so each player always gets something on each drop) and give them the option to Keep/Sell/Trade. The overall purpose of this change is to make each dungeon feel worthwhile no matter what. Details below.
1. Keep - They get to keep the item. This will help in the early game dungeons by giving needed gear to lower level players as they level up. This will also help level alt classes faster since they will be getting better gear as they do more dungeons (since other quest may already be completed and levequest are mostly used for crafting and gathering anyway). As it currently is, lower level classes usually don't get much gear in dungeons, and by the time they get an entire set, it's obsolete. It also helps end game get decent gear faster and avoid the early grind for i-lvl 60/70 gear.
2. Sell - Player will receive gill in exchange for the item. Always a good option if they already have the item, it is a unique, or it's just not needed. Gil would be determined by i-level. The gil reward can be low-to-moderate to avoid exploiting and make extremely rich players (but it sure helps with repair bill, teleport and other suggestions I have below ;)).
3. Trade - Trade the item for seals/crafting materials. This one will tie in to my end-game crafting suggestions. In the early level dungeons, give the ability to trade drops for seals (or gray out the option if they don't belong to a grand company, they still have sell option). We kinda already have this but you have to go all they way to the Grand Company to do it, in the meantime it is taking up space in your inventory/armory.
In primal fights, instead of seals, give the option to turn into new unique crafting materials for that primal so that end-game crafters can craft primal themed gear (with materia slots). This will give a bump to primal fights so that people who don't need them for the relic reborn/main quest can still do them to get materials for unique craft-able items that can be worn or sold (+fire resist for Ifrit gear, +wind resist for Garuda, etc..). The craft-able gear would be similar i-lvl to the weapons you could get with that primal (70 - Ifrit(hard), 80- Garuda(hard), etc...). The weapon drop would still be random as it is now, but in this case the player will always at least get a nice weapon for an alt, or a high-grade material for gear
-Ability to create high-level gear (80-90-100-etc) with materia slots. This will give more incentive to end-game cratfers besides just attach materia and will help the in-game economy (remember we can trade items for money now with the new loot system I mentioned above ;)).
Imagine this scenario: I keep running dungeons over and over without getting the gear I actually want. If I keep trading the drops I don't need for gil, eventually I may just be able to buy that nice i-lvl 90 chest piece I wanted from the market place (besides also having the option to trade allegan tombstones for other gear). This creates an incentive for crafters to keep crafting new high level gear and also farming the high level mats needed (see primal fights above) to create that gear (or buying the high level mats from the market place, driving the economy and helping gatherers).
These craft-able items will be different from the ones that can be obtained from allegan tombstone trade and should not be easy to craft but will yield big rewards since they have materia slots to help create specialized builds. For example, The craft-able piece will come with what I consider main stats (strength/vitality for warrior) and also 2 materia slots (or 3 if it's an HQ item) for secondary stats (parry, determination, critical, resistances, etc..). I think this will bring an additional level of excitement into character builds.
Also, crafters should be required to undertake moderate-to-hard quests to unlock these high-level recipes for these items (after all, it should not be easy obtaining these, driving value a bit). To use as an example, the primal gear I mentioned above, you could just have a quest that requires you to beat said primal and get his unique crafting material (or several of them) to turn in so that the master crafter can teach you how to build that unique gear set with them.
In closing, I think Square-Enix has done an outstanding job with this game. Each major patch opens more options on how to advance in the game and I think these changes I'm suggesting will add even more exciting options into the mix and really pushing into a bit more modern gameplay without taking anything away from the game.
You can edit your original post to go beyond 1000 chars.... TL;DR