First, I'll start saying that the rebalance was more oriented to late game in my mind because even the vanilla game wasn't so bad in the early game it was later when your party outmatched enemies, so I don't expect the early work the way I thought but I hope later on does. Even so I might be wrong.
MP costs for some intial abilites are so high they can't be used, leaving some jobs with nothing to do.
For example, the beastmaster, having bestiary and chocobo song require so much MP, that at lvl 9 with its mp growth, it still can't use any of them.
Or divine aid, the paladin ability, my luso is lvl 10 with 86 MP and still can't use one of the first abilities available as a paladin.
The archer's black arrow also costs a lot of MP, and it being like the second ability available to the job (after focus), makes the archers have nothing to do but autoattack (or change jobs).
I imagine that further down the game, these costs will become not as important since probably all the units will have enough MP for the abilities, but it makes the early game feel a bit limited in jobs and actions.
Some abilities turned out to be better than I thought and they should not be available so soon. I'll replace them for one with a lower cost, but is not easy because in order to make Full MP. I can't expect all abilities being fully usable at the beginning but it should not be so limited. I'll work on that.
Concerning point 2:
Did you consider the stat base? I mean, the mod is designed so the initial election matters. If the base job of your unit is Black Mage, they are going to start with MP enough to throw one thunder. 100 MP - 99 MP = 1 MP then they recover 50 for 51 MP and can't use magic that turn and they need to wait, but that's theory of level 1. Also they'll have a good Mgk stat base. This encourages you to recruit new units to make them fit in a different role that you might me lacking in your party.
Also I can assure you that a proper mage is going to deal more damage than any other unit since they got AoE, their Mgk growth is as high as those on Atk, elemental factor, they can get a lot of bonuses with passives and items, etc...
Regarding identity crisis I need to consider your observations. The Mgk growth on them was so they can be a springboard to either a physical class or magick class. Since if they have issues in either of them if you want a Fencer - Green Mage, you might encounter yourself with leveling really bad on Atk because of your choice. Yellow Mage gets strong Physical and Magick abilities. You will discover them eventually

Since I can't make an attack scale with both Mgk/Atk, I try to give both to a class so they can take advantage of foes resistances, that makes them weaker but more flexible. However, I might give extra stats to those classes that lack in potential, not much since it could be exploited for extra gain.
Point 3: Items expensive is good news to me. Definitely, you don't need to get everything you unlock.
Point 4: Animist only one ability sucks, I need to check that.
Point 5: Kunais, are supposed to be now items in weapon section, because they are used to throw and do dmg.
To be honest, this kind of feedback makes me want to talk with you actively if you are okay with adding me to discord, feel free to add me or we can go to IRC here. If not it is alright as well.