Martial Arts aren't qualities, never have been. You have styles and techniques, which have set costs.
Sure, Martial Arts aren't Qualities, they're character abilities or modifiers to existing abilities that cost Karma from your initial pool or gained in play. Totally unlike Positive Qualities.

And I've seen Ways handled differently at different tables. Some GMs (and Missions) count them for all intents and purposes as regular core book Positive Qualities, but I've played games where the GM went with what the Freelancer said he intended where they don't cost double after play starts. RAW/RAI.
Anyway, it wouldn't impact the game significantly if all of these things were called Positive Qualities and used the same rules. You'd need to juggle the Karma costs in some cases, but it doesn't add anything to the game to have these different abilities have different rules for acquiring them.
I return you to your Alchemy optimization thread, already in progress.
+1 to Mirikon's "Spell selection goes a long way..." If you're just splashing Alchemy or going Enchanting Adept, spell selection is key. Combat Sense, Deflection, Increased Intuition, Levitation, Shapechange, Barrier, Mana Static, ect, ect, ect. Anything unopposed goes right to the top of the list.