When TBC was new, the FULL game required questing from the ground til L70 (L68 for druids and let me vouch for the fact that flightform felt like cheating for 2 levels). When LK was new, the FULL game required grounded questing until L78 and they used lots of caves, tunnels and buildings to force ground questing in many of the upper level quest areas. Cata was not grounded other than as a gold sink and questing was much easier in some areas because of it. MoP was forced grounding until 90 as well and many quests become trivial as soon as the toon obtains flight.
No question that flying is a lot better than sightseeing flight point travel... It definitely is. They could fix that; sounds like that is part of the WoD design plan. Doubt they will change any paths in previous content. Even less chance that any kind of flight restrictions are added there either. Blizz gets nothing from changing those areas except for making them easier to powerlevel alts.
This could the first xpac where flight has a much higher entry barrier set... Something akin to a maxxing rep in multiple factions, or it may be blocked until the following xpac. It would be nice if they came up with another tech that made flying risky. Your energy would be far better spent suggesting innovative ideas for that rather than fantasizing about some conspiracy to make pay extra cash to break the WoD questing content. Too many employed players like me would gladly screw the rest of the player base in a heartbeat. Just because Blizz is right about flight, wouldnt stop me from abusing it ;-)