- More stats to choose between on gear. Critical Damage, Mp Regen, Tp Regen would be the three I'd choose since everything else is pretty well represented.
- Raids being changed to have 3 bosses, as you've said. For one, it makes the raid more of an actual spectacle (some time investment required once you learn turns). For two, it gives a better chance at loot, even at the cost of progressing faster.
- More variety of gearing options. One set of raid gear, all of which is 5 item levels above tome/other current level gear. One set of Tome gear at current item level. One set of alternative 'alliance' raid gear 5 levels below current item level. Alliance raid gear has one or two slots, and can only be melded that number of slots (cannot exceed 2).
- Cooldowns removed when you wipe. (This is something that should already be in the game).
- After that change above, it'd be way more viable to have 10 minute cooldowns in the game. Cool skills (Level 60) that are really flashy, and greater reinforce the strengths (and maybe even the weaknesses) of your Job.
- Multi-hit weaponskills/abilities. If your skill animates and looks like you should be hitting the enemy twice, split the potency (which may buff most attacks naturally), and have it hit multiple times with x potency per hit.
- Phoenix Down is able to raise a party member, but has a cast-bar (slightly less cast time than raise, can only be used once by every party member per raid).
- When you hit level 60, your Job gains a new name (for example Paladin->Holy Knight) and a questline that unlocks 'slots' for your skills.
- Skill Slot system. 2 per skill. The slots can be filled with skill-based materia. So instead of stat points, this Materia has skill-related bonuses. "TP Regen on hit", "Chance to critically hit +%", "Potency +", "Defense +" would just be a few of the basic materia. Then you'd have SPECIAL materia you could gain in other ways, like quests or high-end raids. Those special materia augment things like, "Jump distance + 5 yalms", "Goad effects all party members, less TP regain", "Trick Attack duration +5 seconds".