The secondary attribute only costs 5 Karma per rank (similar to how core-rules Mystic Adepts have to pay 5 Karma per Power Point), and with the spells trade-in, both MAs and VMs get 5 Karma less worth of stuff on the higher priority levels (+2 Chi/Magic, -3 spells; or +1 Chi/Magic, -2 spells) than the core-rules Mystic Adept. The biggest reason to put the primary attribute at 6 at Priority A is to not penalize Metatype priorities that start with 0 special attribute points.
Making both attributes cost special attribute points (which I think is what you're suggesting) would penalize MAs and VMs too much compared to the current system, where they simply pay 5 Karma per Power Point compared to 5 Karma per Chi rank (as VM) under my houserule. My goal isn't to nerf them, but to make them more fun to play while not deviating too far from the core-rules mechanics.
Well, part of the problem with mystic adepts as in the core rules is that they have all but one mage ability, all of the adept ability, and sacrifice nothing for it (ooh, they can't astrally project - with all the dangers GMs spring on mages that try to astrally scout, it's a crapshoot anyway). At the core, they give up very little for a lot of benefit; that's why minmaxers gravitate towards them.
I went back to the core idea of a mystic adept when they were first introduced - that they split their power between slinging spells and channeling qi - when I suggested that their attributes match their non-magic counterparts. With your pricing, picking a mystic adept puts them at near-parity with a normal adept or mage while also giving them (effectively) priority C in their non-speciality. IMHO, they should
not be the equal of a mage or adept in those class specialties; they're dilettantes, dabbling in both worlds, and their values should represent that.
As of now, they don't, and that's why they're munchkin bait. Your method comes close to fixing that, which I like, but it doesn't go quite far enough.
Also, no other magic class can spend Karma points on improving their Magic/Resonance; why should mystic adepts get a free pass to do so instead of using Special Attribute points like everyone else? There's a reason it's a
Priority system; you have to sacrifice something if you want to play a troll mystic adept who kicks ass at slinging mojo and, well, kicking ass.
Part of the problem with mystic adepts back in 2e/3e is that they had to Initiate to raise their ability (which a starting character couldn't do) leaving them WAY weaker than their other magic counterparts. Special Attribute points address that neatly.