You are more than familiar enough with the game to be smarter than believing this nonsense. The entire concept that you can "shortcircuit" any form of content outside of climbing/jumping puzzles without the devs being able to do anything about it is utterly implausible. If they are scrapping the transit system for the sake of jumping/climbing puzzles then god help us all.
In terms of the questing experience, you know very well that quests like Bashiok's strawman example are very few, far between and generally contain subquests to kill X of the named mobs henchmen or the quest hub contains side quests that force you to poke around on the ground to complete.
Single target quests don't exist in a vacuum and flying over a bit of trash didn't render all those level 90 dailies that everyone bitched and moaned about in 5.0/5.1 in any way trivial.
If we're losing flying for the sake of being forced to kill a bit more trash on the ground, then we're not gaining very much.