The main problem is that FFXIV is a modernized MMO with veeeery careful tuning to ensure that a well-played job performs similarly to others in its role. FFXIV also adheres very strictly to the MMO Trinity of roles, so you can't have any particular job that outclasses others.

FFXI is a very outdated MMO environment, where things are made for the sake of flavor rather than practicality. It also doesn't care one iota about the Trinity; there's nothing stopping you from forming an entirely ineffective group of jobs. (and indeed it's very LIKELY that you will if you don't carefully sculpt your alliance)
Heavily customizable content like PUP and BLU in FFXI's outdated environment is okay because people can and will make tons of varieties of builds, with vastly differing effectiveness in different situations. That's fine there, because holistically the game is 'looser,' in fight difficulty, tuning, DPS checks, etc.
In a modern MMO like FFXIV there's no point in making a ton of customizable content for one small subset of players. (a single job for instance) Suppose that you bring back PUP as a DPS. Very soon players will find one or two "optimized" DPS builds, which might end up blowing other DPS out of the water. Because this is a modern MMO, those builds necessarily MUST be nerfed/reworked so as to bring PUP DPS back in line with DRG and MNK. This process repeats until eventually there is likely only one remaining competitive PUP build, or a handful of exactly equal potency. If you don't have one of those specific, carefully-crafted builds, you will be a pretty useless DPS. SE tunes fights under the assumption that the damage dealers collectively do X DPS, split 2 or 4-ways among relatively even jobs, (plus tank damage) and it's pretty clear from playing how carefully-tuned these things are. If you bring any PUP build that isn't the absolute best of the best, you're deliberately reducing your party's chance of success.


tl;dr Making heavily-customizable content for jobs is a large amount of man hours spent in design, followed by a large amount of man hours spent in rebalancing, with the end result of a job with effectively one 'real' build anyway, a build that SE will have to assume everyone is using when they make new fights. They could just do away with the middleman and make it with one build to start, and make that playstyle more interesting via other factors (see: stances, charges, pets, combos, etc)