Ideally the section bosses would include a single mechanic for the alliance to learn - these bosses would introduce the mechanic and require the group successfully execute it to move on. All these mechanics (3 Section Bosses) will be present in the final boss - personally I would like mechanics such as the following:
a) Enmity resets - testing your tanks snap threat and ability to control the boss.
b) Adds - preferably something similar to the Dragonkin in the Hydra fight - if DPS is too slow or negligent the boss will be buffed up.
c) Steady healer checks - high consistent damage requiring timing and teamwork.
Job-Bosses:
Each of the "additional" Job-Bosses should be that Job on steroids. For example a PLD-Job-Specific-Boss would utilize Oaths - Sword Oath making him vulnerable to DPS, but hard to survive - do too much DPS too quickly and it triggers a Shield Oath swap making him easier to tank and heal but cutting DPS significantly - doing so purposefully if the Tank/Healers are having trouble or low on MP allowing players to control the fight - eventually shifting back to Sword if Healers/Tanks are at high MP/HP percentages or after a short period of time. Hallowed Ground being constant from 50% and lower making him alternatively immune to Physical/Ranged DPS and Magic DPS - even reflecting immune damage back at negligent DPS. Being able to self-heal if not interrupted by Stuns or stopped by DPS breaking the cast as the fight goes on. Mechanics that would make sense and be challenging - but not one-shot or completely foreign to the player.
Another idea: A boss fight that puts you into a 16-bit old-school FF fight with menus and turn based combat - playing exactly like classic FF games (EX: FFV). I think this would be really fun - been wishing for something like this since the SQEX FFXIV 16-bit Titan fight video.
PS: If you can't tell - I am not overly enthralled or impressed with FFXIV's current content nor it's approach to encounter design.