The D800E is 'leagues beyond' for literally one thing, and that is absolute acuity; the D800 is just more advanced, that damned AA filter makes a huge difference (see DxOMark for the most pertinent, if not the best, examples). The challenge here is that the end-product difference is usually so very small unless someone is shooting for absolute acuity- i.e., shooting at low-ISOs, using top-notch (which in Nikon-land usually means not Nikon, same for Sony, sadly) glass, and shooting in such a way as to absolutely eliminate subject movement. If this doesn't happen, the differences between top-end systems disappear.
The trade-off for working pros is that the 5D III delivers what is needed- enough resolution, enough FPS, the best (or very slightly second best behind the 1D X, possibly third behind the D4S, TBD) AF, and access to the very best lens range available (Canon and third-party EF included). I see this time and again.
Now this is no slight against Nikon, Sony, Pentax, Olympus, Fuji etc.- this is just one that Canon knocked out of the park, unlike the 5D II and predecessors. It is 'just right'. And note that the rumors (or facts, I'm not sure) surrounding the 'D800S' update tend to gravitate on those aspects that fall short of Canon's most balanced camera.
And note that I don't own a 5D III, rather an in most ways more limited 6D; I'm not a working pro. My 6D now costs about what your A7 did, and for what the 6D gains over an A7 I'd consider it a reasonable compromise, and of course the A7 is a reasonable compromise in the other direction.
But that's not where Sony's challenges lie; though they are systematically pushing up against those challenges in a number of areas that you state. The RX100 III will be the compact camera either to get or to compare against; it's perfect, from my perspective. And while the A6000 is part of a system that isn't perfect, it really does represent the culmination of what Sony has been working on in the E-mount arena, and their continued investment continues to attract third-party lens vendors, unlike Canon's EOS-M, which only just now attracted it's first third-party AF zoom- an 18-200 from Tamron, of all things.
So yes, Sony is innovating themselves out of their quagmire, and yes, they're gaining much needed and deserved mindshare. I know that I rail on Sony, and I apologize that I haven't recognized what they've done right; I've tended to focus on where they could have (and rightly should have) done better, for example their FE lenses, or their kit lenses for the E mount, rather than some of their successes. I'll work on that