Several pros have spelt out that they switched to Nikon for the D3: namely its better AFC and low-light shooting. Comparing the history of new features vs tweaks of D3 through to D5, and now to the D6 tells us more as to perhaps how Nikon have named these cameras:
https://photographylife.com/nikon-flagship-dslr-comparisonLooking back at the flagship D* DSLRs, the improvements have largely been incremental eg fps, although one might quibble 9fps > 11 fps is significant to capture the right gestures at a critical moment (e.g. golf swing, bird landing).... the faster fps the better to grad the "WHEN" can be vital. A New AFC engine is the Mega-Tick of the great leap forward: thus D3 and D5 versus D3 and D4 upgrades. All the tweaks to video etc are merely minor, nice but sidelines - ie none = a Mega-Tick. (So perhaps Nikon work on the maxim of if it ain't broke, don't fix it.) If the AF engine gets redesigned / upgraded then it's a new flagship. This makes sense given the primary users of these cameras. As those with experience tell us here, the FX AF sensor had its limitations, and so it could be argued the D4 did not justify its moniker after the three D3 versions, but Nikon improved the D4 sensor.
Perhaps, the tighter girding of R&D over the past few years (with Z System urgencies and demands) explains why they did not merge more of what we see in the D780. But, again, which Pros really need more of such features?
Improved networking of the D6 is the other Mega-Tick why it's no D5s.
D3 > D4 > D5 each updated the sensor. With the D5 > D6 it's still 20mp - Oh the horror of horrors!!! but we do not YET know if these sensors are the same. If Nikon has improved D6 IQ at end of the of ISO range then another Mega-Tick. Especially if ISO100 gets better DR and the low-light ceiling has "darkened". If it turns out a +ve at either end (better both ends) then Wow, and Wow! This will be significant for actual photographers of sports and wildlife, who push the extremes.
Nikon pulls off bizarre blunders time and again, eg no grip with controls on the Z cameras. Considering how the D6 has turned out, viewed in retrospect the D6 teaser videos are even more bizarre than they did pre-release. Why the hell didn't we see glimpses of the new AF in action (using tested prototypes) - and in low light too?!?
However with the flagship FX DSLRs aimed primarily at Pros shooting top level action events, the R&D has consistently delivered a rugged tank of a camera that delivers, and above all a camera "that leaves nothing to chance" wrt capturing subjects in action scenes. The AFC is the crux. So we read the D6 AF sensor is now Multi-CAM 37K (D5 is Multi-CAM 20K), and layout of the cross-type sensors and software are major upgrades. If tough testing might in fact turn out to obviate the official claims, then there ARE problems. If the AFC in the D6 is indeed a significant improvement, then the D6 is NOT a D5s contra Mr Hogan in his latest essay insinuating Nikon is too proud to call the D6 a D5s.... He should know better.