I see your proposal for bonus objectives that changes bosses behavior, dificulty and reward based on the party performance along the dungeon as viable. Back in Aion we had a dungeon named Dark Poeta in which the last boss was decided by how many point the group accumulated during a dungeon Clear (it was a mix between time and number of enemies killed with one or two optional quests thrown in). The bosses were increasingly difficult and dropped better stuff.
I can see FFXIV implementing something like that if only they made Dungeons a bit wider and less linear - allowing players to choose between killing or avoiding certain objectives and packs of mobs. The End boss could drop a variable quality and amount of currency depending on the party performance (going from small amounts of Law tomes to high amounts of Esoterics and, in the highest difficulties, even Alex normal / hive tokens or Tokens to Exchange for itens to enhance eso gear)