We have all seen the discussions, about why popup-flash is left out on the pro bodies from Canon. Those in favour of leaving it out says it is because it can break, and it is not a "pro feature".
Is the 6D a 'pro body'?
IMO, it's a marketing decision. Canon wants your money. FF bodies (from Canon) don't have a popup flash. FF bodies cost more. Canon figures if you need a flash and can afford a FF body, you can afford a Speedlite.
The 6D is pro in the sense that it is full frame, demanding EF-lenses. Which sure sell at pro prices
If it is a marketing descition, it sure is not a good one (IMHO). Portability is more and more an argument being used, with all the mirrorless cameras making their entry into the full frame market (Sony). Lugging around a speedlite in adition to a big dSLR is... annoying. Yet another thing to bring along.
I think it would be wise to implement a popup flash in the 5D4 (and/or 1DxII), and make it special, not just a simple popup. Like others have said, HSS, flip/tilt functionality etc.