I understand that, I think. But in most TSR worlds, humans are the apex predators. Nothing is going to march straight into Waterdeep because humans will stomp it into the ground. In a E6 world, if there's much big nasty stuff around, why isn't it running Waterdeep or has destroyed Waterdeep?
Well, that's the plot.
Really, humans aren't the apex predators: the PCs are.
The Orcs do come out of the mountains and attack Waterdeep. If it weren't for the archmage protectors backed by their deity Mystra, and others; or Halister Blackcloak of Undermountain, who likes humans because they enter Undermountain so his pets can eat them; Waterdeep would have fallen. I think it may have done so at least several times before Ed Greenwood and his friend made up the apex predators of FR.
Orcs are just one example. Ogres are another. Hobgoblins. And, yes, Dragons.
Er, an Adult Red Dragon (from Pathfinder) can basically autokill any 6th level character with its breath, force them to make DC 21 Will save not to run away (i.e. a 6th level cleric might bring that tp 50/50), has a 29 AC, DR 5/magic = actually hurting it is going to be extremely rare, and 212 hp = even if you can hurt it, it's not going to make a difference. And Speed 40 / 200 flying, so even if you can make a plan, it can outfly it. What more do you need on stats? This is a tarrasque--completely unkillable short of a wish--in a E6 world. If it shows up, you're either going to try and engage in diplomacy, run away, or use the Macguffin against it. Go ahead and wing it; the stats just don't matter.
Exactly. That's the point.
But the gods have stats in D&D, including two books focused on them: FR's faiths & Pantheons, and of course Deities and Demigods. Heck, Monte Cook's Call of Cthulhu d20 has a set of stats for Azathoth of all things (and the other Mythos members, like Cthulhu and Nyarlethotep), and I guarantee you no PC of a regular game will fight that guy for more than a round.
Setting is more than what they would do normally. It is the perilous situation the characters find themselves in *right now*.
Dragons sit on mountains of gold. They sleep there for centuries. The PCs could get that gold if they figured out a way to stop the dragon from waking up permanently. Maybe they just have to use dynamite on the Lonely Mountain, cave in the roof and crush the dragon. Maybe they could quest for an artifact that could open a portal to the plane of water and *drown* the fire-breathing dragon. Maybe they need to make a pact with the Frost Giant Jarl, who sits on his throne in Jotunheim waiting to fight Thor at Ragnarok.
Saying "it's E6: so there isn't anything beyond 6HD" doesn't make a good game, and it isn't E6.
E6 means HUMANS aren't above 6th level.
That doesn't mean that, in ancient days *other* creatures mastered magics incomprehensible to humans, and left their magic lying about in ruins. Who ruined them? Why, the Terrasque did when it escaped; or the more powerful Red Dragon, who casts unspeakably powerful spells as a part of its nature.
There could even be only "a" Ancient Red Dragon Greatwyrm, the mother of all dragons. A critter like that *should* be so fierce the PCs wouldn't stand them. And there's only that one.
All the top-level dragons could be "the" Council of Wyrms.
As for why they're not just coming down out of the mountains and killing all humans...
This link discusses the Underdark and why we're not swimming in Beholders who've already destroyed the world. I am convinced it is essential reading for setting design in E6.