Content won't be broken by flying in most cases(things like small puzzles to get a chest comes to mind but that's not really important). The problem with flying is that it allows you to skip everything in the world outside of the 10 mobs you need to kill for a quest. It's simply too convenient as it makes the game into mount, start flying in a direction, alt-tab, tab back in, fly straight down in the middle of anything, kill a mob, repeat. With the way things are right now you'll at least have a good while to go through the world and see the content that's there.
As for the mobs on the ground it makes sense. If you walk into a murloc camp there'll be murlocs on the ground. You can't throw mobs in the sky everywhere and expect it to look decently. Other than it looking decently it won't make sense.
Another thing is that the reply i made was about making flying somewhat challenging, which isn't really doable right now. I think that the current model where flying is unlocked partway through an expansion is good because it allows you to see things in the game and brings the convenience of flying back at some point. While you want to be able to fly from the start there are people who don't and at that point it's a matter of opinion more than anything else.