First point - I think you might be able to argue it works quite well to have this sort of dual system. Obviously one of the concerns was if they limit the skills learned to a small selection (which creates the best balance and ability to make a tight gameplay mechanic) that it wouldn't feel blue mage-y. Well, what if I told you that you could learn hundreds of skills and use them but you also were able to compete in normal content in a balanced way? Does that sound pointless? So by being Advanced Blue Mage is both a job and to the fullest extent possible also "Blue Mage". Obviously a response to that would be "yeah well I can't use all of them in that balanced content now can I? hmmm?" lol but I'll get to why it'll still have a point and be helpful to the community~!
To add because there is a sort of "what's the point?" I'd argue the current point of blue mage is very weak .. and while we weren't discussing it I'd like to slide the point I want to "inject" into blue mage while I make suggestions like this (which hopefully makes the argument for Advanced Job stronger and more poignant than being limited in it's current state).
That is Blue Mage, obviously, would come in two parts - the first part would be unchained and rather unbalanced. Gameplay mechanics for this would revolve around trying to make a great solo experience and enjoyment of the open world, specifically old content (BLU "sort of" does this now, but imo not nearly well enough). With some suggestions I've picked up over multiple threads I'd suggest this unchained (limited side of blue) doesn't use gear score at all but rather ranks your blue mage based on # skills learned and their power - such that blue mage's power comes from it's skill specifically and ANY PLAYER can enjoy the side content of blue mage to it's fullest without spending a single tomestone on Blue Mage (this is for the limited side only, the main side will require you to gear up - of course). This allows Blue Mage side content not to be locked behind playing blue mage as if it was your main, this is really nice and helpful for the community (I think). If people are worried about gear sales you could always make it so there is a vague relation to gear and blue "ilvl" such that if your gear is for level 50s you can have a max ilevel of 150 (so the quality of the gear doesn't matter, only the minimum level requirement - meaning again you don't need to "main blue" to use side content blue).
Second part would be the main job, obviously a job as one would expect but using the spell book and learning gilded spells (spells in the book that have two variants, one balanced one not). Flipping the job stone would dictate whether you have gilded variants (and are locked out of non-gilded spells), as well as your ability hot bar and equipment (almost but not quite like "two jobs"). Blue Mages would obviously level easier than other jobs but they'd spend more time going to get spells, to counter balance the ease of leveling. I do suggest some changes to how skill chance works to prevent terrible luck but I don't want to rewrite my timeline thread lol.
So now you have current version:
Get seals, collect some stuff for the sake of collecting, doesn't really solo content better than anything you already have.
VS
Side content everyone can partake in (like before, but smoother even), destroys OLD content (solo) which can help people who missed out on stuff - even like Eureka (is not allowed into current tier!), & behaves as a different style job where in the focus is not leveling but gathering skills, but as it is a main job it is a job that will carry forward forever (like other jobs). That also comes with the peace of mind that it wont be forgotten :3.
I feel the point of existence is much stronger with the later as it allows people to hit that old content hard even if they're leveling jobs that normally don't do well solo but also allows a job that uses similar resources making it more cost effective than designing an entirely new job. At least personally I'd find far more use out of Blue Mage if it was like that.
As for the second point you made, you're right that we're focusing tightly on blue mage and I know some don't care about the future but actually in my timeline thread I detailed Beastmaster and Puppetmaster following the same Advanced Job route that I want Blue Mage to follow. In that these advanced jobs bring new content to everyone, as a form of side content/mini-game, but they also bring a new job to the table that some players will really want to play (some players play all jobs, good for them, and some players want a different style of job to "main" - higher chance they'll find their home then).
I do admit there are some jobs I have a harder time imagining them to be Advanced successfully, but Blue Mage, Puppet Master, and Beast Master are not jobs I think have that issue. Given that you go "Advanced" at least, using the limited side of advance to fully narrate the job in a way that might be unbalanced but fair because everyone can take part fairly easily and then the main side to make it a job as one might see a job.
Together it, hopefully, would be a much more detailed picture that satisfies more than just something like "beastmaster, it's pokemon but worse".
I understand your hesitance because obviously I'm not asking for a simple change, it's a whole freaking job to design lol, but hopefully at least it could be like "I wont hate that if it happened, even if I'm not sure they'll do it". Although to be fair you've already sort of said that haha - so I guess I'm just trying to sell you more on it.
Even if we disagree thanks for reading.