This isn't directed towards you, it's just that you are the only one who has posted these concerns, though a lot of people have them, this is addressed to everyone.
My biggest problem with these how they *were* and are in other games is: Why do you think a skill that enables you to attack with skill without a weapon should give you some fantastic bonuses to your modifiers or any abilities above and beyond other combat skills like Small or Medium melee? They shouldn't.
Small and Medium Melee give more damage because you are using a weapon in hand, much more deadly than a hand to hand attack. On the other hand, you have to be holding a weapon to use them.
Trained Fighting and Fighting Mastery give less damage, however you do not have to be holding a weapon to use them. It's a tradeoff.
The study of Martial Arts is a lifestyle, not one single all encompassing skill. Most involve religion or philosophy, faith in a deity or ones abilities, athletic training, development of Body, Mind, and Soul. These should be overall character concepts around these skills and not covered simply by a medium and high XP cost skill.
Do you get any bonuses for studying Medium Melee? Even though Iaido and Kenpo are Sword based Martial Arts styles? No. So why would/should you expect them from an unarmed style?
Why should any ability replace a +6 Attack? There's no reason anyone should expect any skill to give you that sort of bonus when no others do, especially a hand to hand attack skill. Just doesn't make sense for Catholic Priests, Seamstresses, Street Urchins, Beggars, or Bankers to have an Eastern Martial art simply because it gives them a bonus to their modifiers.
Peronally I think it's a shaft. If anything, force it to BG only skills. That way you can deny as many people as you want, but still say you're being fair. I can't imagine any “ability” replacing a +6 to attack. People spend good pts for stuff like that.
Can I deal ? yeah. Do I have to like it ? Naw. Will I shut the hell up about it ? Probably. I'm Gemini, I get bored easy.
Like I said before, hopefully whatever replaces it is just as enticing as those numbers are. I don't know many people that buy melee fighting styles for anything less than those numbers;when they can so easily turn to a ranged weapon with abilities of their own, and stay clear of an axe to the head.