So far changes like merging magic and innate abilities looking great 
Maybe Knight's Equip abilities could be dealt with too? I'd personally paired Armor with helms and gave it 250 AP, also merged Sword and Shield in one for 450 AP or so. Because well, it would be nice + 1 free slot 
Now, Monk, it's really all good set, though 3 abilities with different HP bonus kinda sucks. I'd threw away 20% at least and made 10% into 15% cost more AP, like 150 AP. Less grind, also not leaving only 1 because would be nice to have early 15% for different jobs rather than going all way to costly 30%.
Blue Mage Check is redundant with View ability, Check must go completely. Also would be great if Learn would work like for Strago - character with Learn is present in battle and not undead/petrified/blind/paralyzed/dead than he learns ability on whomever it is used(not only on him).
Red Mage after merging his magics in 1 asks for something useful. Could be nice to have ability to double damage of next spell.
White and Black Mages abilities to give extra HP aren't needed with Monk having same. White Mage should have some MP regeneration instead and Black - 30% MP.
Berserker sucks, but gives axes and high attack growth. I have 2 propositions to unsuck him
Make Berserk an action command instead of auto status on battle start. And give him Umaro's Tackle - physical attack ignoring defense.
Time Mage have nothing interesting on him and with some slots freed after magic merging 1 new ability could be squeezed in. I propose Last Haste, when only 25% of HP left gain Haste status. Should work nicely with him and other jobs.
Summoner... Well, Half MP would be nice. Making call cost like 250-300 AP and Half MP an ultimate ability for 500 AP seems decent.
That's all for existing jobs I can think of to make 'em more interesting.
I added line breaks to your post, you should too in the future.
If passives are automatically equipped on every job after you learn them - and a lot of spell level skills are being consolidated - then they can be as granular as vanilla, or even more so. We are talking about freeing up maybe 20 or 30 skill slots. In reality, I wouldn't suddenly forget how to use a shield if I decide to become a martial artist. Why should FF5 be different?
I think Lumiere has the right idea for spell level skills - something less fine grain than vanilla, but which lets you get the bulk of the skills in a few chunks. My idea was too much. My biggest concern is getting more skills into skillsets, which limits non-caster classes the most.
Do Check and View have the max HP limits in this game? Is it possible to fix that, or instead check current HP and return "Too high!" if it's more than the amount that can be printed?
As for your other ideas:
1. I don't know how OP is doing all this, or if any of your ideas (or mine) are feasible. Which begs the question, "How exactly is OP doing this?"
2. While these ideas are interesting, they don't seem too balanced.
3. There are plenty of ideas to draw on in other Final Fantasy games, both with and without job classes.
4. I'm pretty sure passive HP/MP bonus skills stack, so why remove them?
5. While your ideas may or may not be something OP wants to do, they're not bad ideas. If there's a tool to edit FF5, you should make this patch so other people can experience it.
With Mystic knight/Paladin left with 3 abilities(Magic Shell and 1-3? 4-6 magics) would be great to give him Runic from Celes' arsenal as job command, so there'll be something useful to him.
Mystic Knight aka Sorcerer is a sword mage, not a Paladin. Their skills are closer to Steiner than Agrias or Celes.
Celes' Runic is pretty useless most of the time without a complete enemy rebalance, as few enemies use human magic spells.
Runic is global anti-magic field and Absorb Used MP that acts so long as it was used previously and Celes' turn hasn't come up again. This is:
1. Too broad to be useful as it prevents you from casting spells of your own.
2. Too pathetic to rate using it to restore MP unless more spells are caught by it due to more enemies having spells.
3. Too short and uncontrollable a duration to be consistently useful in an anti-magic fight.
You could make it affect only enemy magic, but then it becomes OP - especially if more enemies have spells. You could limit it to enemy spells that target your party to slightly reduce that effect.
You could make it act as a bit toggle, and prevent the caster from doing anything else while it's active and until it absorbs a spell. You lose a party member to block a spell, which is pretty niche and you need to know what's coming beforehand to equip it.
If you make it act as a bit toggle and let the caster resume actions after a turn then it's more useful and worth keeping on your party.
You could make it act like a byte, and store up Runics with each use.
You could tie it to Sword Magic somehow, and have a successful Runic let the caster use a Sword Magic spell immediately and for free. This would make it act like global (or enemy) anti-magic field, Absorb Used MP, and a less automated version of Counter Magic.
And of course I have no idea how easy it is to implement, which it probably isn't.
I would give one additional ability to Mimic too. While Mimic command mimics last used action by anyone, Encore ability should repeat Mimic's last move.
In other games there are two Mime skills.
1. An active skill that repeats the last action taken, as the Mime command in FF5 and FF7.
2. A passive skill that repeats every legal allied action, as the Mime job in FFT.
I'm not sure if #2 is possible, but if it is it should be very expensive.
As for GBA jobs and content, it would be hard to squeeze them in and code even with all those abilities' merging. Instead I propose Dark Knight job using Gladiator's sprites. As for abilities for it: Advance - 2x power attack halving own defense until next turn, Provoke - all enemies attacking user with their next attacks, Dark Art - infamous dark element attack to all enemies using own HP as MP for it, Reach - no damage penalty from backrow.
It's everyone's favorite
If he could be there without sacrificing any other job that would be great enough for me.
No more job thoughts and there're more capable people to suggest everything else 
None of the GBA jobs are interesting, I'd rather get something from FFT or FFTA.