The issues you have with the boss countering your tools boil down to two main things: imprecision and jank.
... Yes?
What do you think I'm complaining about exactly?
Bad game design and broken mechanics.
I
know it's an intentional part of the design design that they take all of your tools away and make you fight the boss head on. I'm saying that that's not a good way to design your game.
The options that the game gives you should be useful not just in the basic levels but also in boss-fights.
The Kunai should do something to the boss. The first two attacks should do some damage (although obviously not as much as the third)
The fire jutsu is hard to pull off, a limited resource and honestly not very useful against ordinary enemies (who are already so easy to kill) so if it's also not useful against the boss, what's even the point of it?
Make it do 1/5th of his hp on hit. Since you can only do it three times at most before running out of MP, that would still force the player to find another way to shave off those last 2/5ths of his health even if you land all three (or to do something sketchy with intentionally getting caught by his rape-counter move to get fucked and get some MP back, which would at least be an interesting mechanical interaction)
As for the takedown counter being 'a trap'
Obviously i'm saying that because the game tells you that it will work if you do it with the right timing, but it doesn't.
The fact that it's not
intentionally a trap (because it's not
supposed to be broken) doesn't change anything from the POV of the end-user. It's still a trap. If you attempt to do the counter, you're just going to be punished for it.
As for there being 'plenty of places to get three hits in', I just think you're outright wrong. None of the boss's moves have such a huge recovery that you can land all three hits. He always recovers and reacts while the ass-slam is charging up, and he'll take off half your life if you get greedy like that.
But that's the point I made, most of the time, he ONLY reacts after you land two hits, and those first two hits don't really do anything. So aim those so that you miss on purpose and only hit with the third one, and suddenly he's not a very difficult fight.
It's just not satisfying that the only way to beat his boss is to lame out his bad AI instead of actually using all of the tools and mechanics that the game has.