Timeless Isle's success was dubious at best.
Theck points out a few major flaws, and I personally see the major flaw of Timeless Isle that it provides little in terms of story, and outside Ordos and the Celestials, it is nothing but insane amount of grind. It felt as an attempt at a GW2-like zone, and, it didn't seem to fare that well in that aspect (at least to me, having played GW2). On top of that, almost nobody from my guild does visit the Isle anymore, bar the short phase when they are gearing an alt. All in all, a continent that would be "a few bossfights, several random encounters and otherwise grind, grind and more grind" sounds like very mindless design, not to mention that it quite butchers immersion.
That's not on topic when it comes to flying, however.
It still will present a problem that players will do most of their travel time in the air. Outdoor activities that were not done much up till now, when there is a convenient tool to get out and be active, won't suddenly be done more when getting to them will become inconvenient. The ballance technically can be stricken, but it is a VERY fine one (otherwise we either get the overload of flight points like there seems to be in low level areas in EK/Kalimdor, or one/two/no flight points in a zone as it used to be in Vanilla), and if the ballance is actually stricken, using the flight paths to travel from point A to point B will have very similar effect travel-wise as flight itself, with the possible inflight interaction with ground (that is, flying down and interacting with ground countent) removed. Of course, Blizzard could revamp flying on a flight path to allow ending the flight before reaching the flight path's end, but that would require a revamp of how the flight paths work. Again, the amount of effort required for that to happen makes it quite unlikely.