This question seems to get posted every few months. I'm not sure why you are asking
... because I guess that the 1/180 x-sync and 1/4000 shutter limitations on the 6d are not hardware limitations, but put there by marketing to set every spec in the sheet below the 5d3.
Eh, no. Not at all.
The 6D also has a much shorter life expectancy for the shutter.
Put it all together, and it's clear that it's an entirely physically different shutter from the 5DIII -- one that's slower and less durable, and obviously cheaper.
We can surmise that the shutter doesn't move as fast because the maximum shutter speed is slower. That means that it takes longer for the first curtain to clear the sensor, which also accounts for the slower sync speed.
No firmware in the world will ever get those shutter curtains to move faster, unless there's something in the firmware that controls the voltage to the shutter actuators, which I rather doubt. Even if it exists, it'd probably blow up your shutter right quick.
And, as for missing AFMA? Considering the 6D has a brand-new bottom-of-the-line autofocus system, I wouldn't at all be surprised if AFMA relies on some of the circuitry in said autofocus system. Considering that it's the autofocus system that drives the lens and that that might not be controlled by firmware...well, if so, you won't be getting AFMA on the 6D.
Really, I don't think Canon is in the business of crippling products with firmware. I think most of the "crippling" has much more to do with manufacturing practices, design tolerances, and that sort of thing. That is, the camera is cheaper because it's more cheaply made with cheaper parts assembled to lower standards. It's still a great camera, but it's not as highly refined as the 5DIII.
And isn't that exactly what everybody has been asking for? A no-frills, cut-all-the-corners, consumer-oriented full-frame camera?