That's because your wish is locked into a specific setting. Instead of Job locking, which is too restrictive, IMO. Class lock instead. This, coupled with the idea of being able to have multiple jobs per class eliminates that concern.
I wouldn't even put it anywhere. Speed Runs should be for timing events in which speed makes sense to the lore/plot of the game and nothing further. Perhaps a timer to prevent from holding up the instance server, but the timer should not have any significance beyond that. - or, as a compromise, have speed runs be one of many factors that cause chest to drop as a point total, as I described earlier.This has more to do with loot and dungeon design. I'd hope they'd do away with the silly timers, abolish speed runs altogether while putting in timed events in dungeons where appropriate.
MP pools, magical stats,etc in FFVI were not equal. They could be MADE to be equal, but the lowest common demonimnator in the game - the Esper system which taught magic, altered stats, etc, has a similarity to the class system, which allows us to socket from any class we learned from.My point comes entirely from how parties would split themselves up while still working with a reasonable raid composition. Granted, this entirely falls on class design, ability spread and DPS, which I'd like to see addressed first. You seem to also miss the fact that the Lowest Common Denominator in FFVI was the fact that everyone could learn the same magic, which means that regardless of character you could have someone in charge of heals or have everyone able to heal, buff and so on. And I mean heal/nuke/cast reliably without stat limitations and discrepancies in MP pools.
So the class system becomes our lowest common denominator in FFXIV, and my compromise to your Job-lock system makes the entirety of the FFVI style dungeon possible, as you can blur roles for smaller battles. A Paladin from one stage of the fight can become a 'Dark Knight' (or some other job) as the parties merge, or vice versa.
You're also assuming we're wanting a Tank Party, a DD party, and a Mage party, all with their own support focusing on just them. But with classes that can take multiple jobs, that means they can take multiple roles. AND, it might be better for the group as whole to not have such a focused center as the end boss may be multiple tough enemies instead of just one. Put simply - we don't know if such a dungeon would follow the conventions you're referring to.
In the end, a dungeon built like Phoenix Cave/Kefka's Tower might actually be a good shake-up from the norm - something we really need to be honest. And as this is supposed to be some sort of fan-service game, I can't imagine a better dungeon crawl in Final Fantasy. Phoenix Cave and Kefka's Tower are by far the most memorable of them.