alphawhelp's point about 'where does it lead?' is a good one. It's one thing to take guns and a martial art or two that allow for extra bonuses when dodging, dodging without penalties for flanking, etc.
It's another when it comes to adding in the extra attacks at lowered penalties and other special abilities of martial arts.
Change of thought, thanks to that: I'd go with his suggestion. TKD and Style.
That is one of my fears. Purly based on MA though your looking at
Aikido: bonus trapping/take down so little bonus based on your weapon
Kung Fu: variable bonus, I can see the damage one being strong but nothing ridiculous for the cost to learn this
Pankration: makes it harder to escape if you trap someone (weapon won't really make this better)
Shotokan: nothing added
Boxing: nothing added
Capoeira: Makes area attacks easier (a lot of weapons already give this bonus as do styles)
malla-tuddha: disarm bonus (also some styles already do this)
Sambo: makes precise more deadly (I think there ways to do this with style/right weapon but not sure off hand)
Kempo: extra attack (which you can just buy for same cost) and lowers penalty for extra attacks (this one is nice and cause for some concern depending on the weapon)
Tae Kwan Do: already allows weapons
Lama: Bonus to defense actions. Without Ki, magic I think this is pretty unique but I don't think game breaking
Grappling: Weapons can already give these effects
Tai Chi: nothing
Kardad: extra attempt at characteristic test. Unique but I don't see it being bad
Xing Quan: situational bonus to attack, not bad but expensive (Can just buy straight attack bonus for -5 difference to attack roll, but without it being situational)
Kuan: Lets you use a weapon as a shield pretty much. You can already buy a module that lets you do this with 2 handed weapons for much cheaper
Soo Bahk: Tons of defense bonuses (and this is the style that started the entire investigation into this idea since I can't find another way to pull it off)
Advanced MA's
Emp: bonus to disarm and can make the attempt whenever you get the right to counter attack. This is pretty nice
Selene: Very strong
Suyanta: Will make ki characters upset. I believe can do this far cheaper/easier though with nemesis or other techniques
Velez: Very strong. Though there are fair cheaper ways to accomplish this using nemesis/ki
Asakusen: Pretty nice variable bonus. Nothing that seems game breaking though
Lama Tsu: Super nice defense bonus. This can make a martial character very strong
Seraphite: almost guarantees an action
Melkaiah: nice bonus to attacks, maneuvers when on the offensive. A bit situational but a real bonus
Dumah: Break all the things. This is super nice against the right opponent
Mushin: Weapon doesn't change this
Hakyoukuken: Ignores armour. This also does mean things to the right opponent
Shepion: Weapon does nothing to this
Enuth: This is just mean (though it is pretty brutual regardless of using a weapon or not)
Hanja: About as strong as Lama Tsu
Godhand: There already weapon styles that let you do this
Rex Frame: Nothing
Exelion: nothing
So ones that I see abusable with weapons:
Hakyoukuken (high damage weapon and only supernatural ways to stop it won't be nice)
Kempo (makes extra attacks too cheap)
Enuth (would make the DC to save insanely high [Though it is already insanely high if you just try to do this normally])
So after doing all that I don't think what I need to do is make an advantage to let a character use MA with weapons and get the advantage as much as a new style/module that is kind of like Soo Bahk. Maybe also look into a few of the ones that give nice situational bonuses to maneuvers (I do like the ones that give bonus to x maneuver when counter attacking).