Because most characters for Missions style games will never raise there skills above 6 that have skills already at that level.
Not just Missions.
There is very little mechanical incentive to raise skills above 6 for any character. The cost-benefit ratio doesn't favor it at 6-7 and gets worse from there. Archetypes that depend on karma for advancement (Awakened, Technomancers) have much,
much better things to spend Karma on (initiation/submersion, foci bonding, spells/CFs). A level 1 Power Focus is a much better investment than raising Spellcasting from 6 to 7, and people rarely buy the level 1; you may as well just save for the level 3+.
Archetypes that depend on nuyen to advance (sams, deckers, riggers) would benefit much more from the karma-for-nuyen trade than raising a skill by one point.
As in 4e, you largely start with the high-level skills important to you, because that's what justifies you getting paid for criminal activity from run #1. Raising the skill cap to 12 was done, I think because in 4e you could start at the top of your field with a 6, and I don't think the writers liked the notion that any character would be at the objective top of their field starting at chargen. Raising the cap to 12 shows you have a long way to go to be at the top of your field in a skill, but the mechanics certainly don't incentivize actually truing to get there.
JoAT is great for picking up a bunch of skills at 1-2 with karma, which is even better for numen-dependent Archetypes because they usually have high Attributes boosted even higher with ware. Pilot Ground 1 may not look like much but when your augmented REA is 10, you just got a pool of 11, which is more than you will ever need unless you try to do cray maneuvers (which you want a control rig for anyway).
JoAT also lets you short skills to a lower priority and pick up the tertiary (but occasionally useful) slack in play on the cheap. Like Arcana for Awakened. It's basically useless except for initiation. So you want to get 1 before you have enough karma to initiate, then after a couple initiations you want to boost it to 2 and maybe buy a spec to ensure you keep making your rolls.