Now I will admit straight up, that this is inspiration from multiple different RPGs, different games, many different systems analysed to look at what would work best specifically in a turn based rpg game, trying to maintain the balance of both power fantasy but also trying to keep it to align with an actual balanced system.
I will set a premise that end game abilities should be equal across all players, meaning that just because you would want to have a Rinnegan Madara Bio, Full Bijuu unlock, or even a custom character that has An AE, paper and say sage mode, everyone that reaches the end game should be on equal footing if they have the same amount of work put in. Additionally, I believe in the idea of a Rock-Paper-Scissors triumvirate of strengths and weakness is a a key part and should remain a key part. I dont think the idea of 'neutral to all' or ;strong to everything' should exist. Its just a key part of any game balance that one thing cannot dominate anything else. Sure there can be Meta's and patches and balances happen, but it should exclusively be obvious just from picking certain characters/abilities that you are worse or better off than others.
The AP system was a great additional and definitely should be kept, but I think it should be adjusted or at least expanded upon, it didnt really specifically limit anyone to specific builds (IMO), and everyone still kinda really just did a jack of all trades type spread. Id much rather see something like class diversity happen instead of bland 'everyone throws nukes' type builds. Id rather see a system where AP is instead spent to use or unlock your kit and give you specialties if you go far enough in it.
The following is a ROUGH draft of a more in depth AP system, that gives more customization which tries to balance a bit more about what people have access to.
As an example, lets say as a Jounin I have 45 AP points, you have the 5 elements, what ever abilities your bio has, lets say its a basic sasuke, so uchiha with curse mark.
With Health, Chakra, speed, Tracking, Durability, Ninjutsu, 'Body' (placeholder) and 'Genjutsu', Fire, Water, Wind, Lightning and Earth.
Each one has a quota to meet to be able to use specific level of abilities.
Eg, to use S rank fire, you will need a minimum of 5 points in Fire. So your spread might look something like
Health: 2
Chakra: 3
Speed: 4
Tracking: 3
Durability: 0
Ninjutsu: 3
Body: 3
Genjutsu: 5
Fire:6
Water: 2
Wind: 4
Lightning: 5
Earth: 0
Sharingan: 3
Curse Mark: 2
Effectively what this spread would be is someone who is proficient in Fire, Lightning, genjutsu has medium skills in ninjutsu, as well as their sharingan and curse mark, and medium build for health and chakra. Notice the 6 in Fire, that would unlock the F ranks, and potentially the first specialty. It might be something like, Can use Fire techniques with one handseal.
Now lets say I complete a few more missions, level up, get some more AP to spend. I can improve what I choose, and if I get to a point where I want to Unlock Mangekyou, it might require something like 5 in Sharingan just to unlock it. Then to get more techniques, it might require 6 or 7.
Once again, this is just a rough draft with a full written copy saved in my GoogleDocs, with full on talent tree system, basically written out.
Personally, I think that one thing that needs to be changed is the whole 'infusions' and passive techniques, I can just see the system once again being 'i passively use X, Y, Z, and now i have two +20 boosts turn one'. This can be incorporated into the AP talent system, where you specialize specifically in an element or ability, to actually master it to do more damage. Maybe you put 8 points in Fire and now you can do fire without hand seals and all fire techniques are passively +20 damage stronger.
I have more to say, but this is just a small excerpt of what id rather see changed or made.