2) Your larger point has been answered, you just don't like the answer. The baddies are in the middle of unspecified large plots that come to the point where someone notices them when the campaign starts and the GM wants to use them. That's not "the villains sitting around waiting for the PCs to show up" any more than than Elvanna was waiting for PCs to show up to rescue Baba Yaga in RoW. Or the Runelords have been waiting for PCs to oppose them before they started coming back.The opposite problem is in someways a worse (and more common) one: Why, with all these high level rulers and famous casters around do a bunch of upstart PCs wind up having to deal with the real problems?
Because these principle forces (Dalkyr, Blood of Vol, Lords of Dust, Dreaming Dark, The Mockery, etc.) have long-running and, one assumes, deep-thinking machinations, the right answer anytime PCs begin getting a little too close is to go to ground. The BEBG is functionally (or even worse, actually!) immortal. Just wait them out.
Or summon a Wraith-strike somewhere else to distract them. And if the PCs are not distracted, so much the better. Now they get to come home to a city full of wraith-spawn.
Khorvaire at least would be over-run in decades at most. Except for possibly Vol, none of the big players want to make something of civilization. They want to tear it to a bloody pulp. Dalkyr, Lords of Dust, Dreaming Dark, and maybe others, are not even as favorable to the races of Eberron as ISIS is to their enemies.
As 911 showed - when your only goal is to tear down - a group doesn't need to be particularly sane or skilled to let loose great havoc. And the BBEGs in Eberron, particularly the ones that can drop auto-spawn "bombs", are a great deal more powerful compared to the civilized folks of the realm, than al Qaeda are to the various nations they oppose.
As to your implication for other, more usual, Fantasy RPG Campaigns:
Why doesn't Elminster rule Abeir-Toril? Besides not wanting to, he's trying to keep the lid on Manshoon, or Fzoul Chembryl, and such.
What are the Lords of Waterdeep up to that they can't handle crisis X? Besides travel and infighting (they may all be Lords of Waterdeep but they are not allied except only in that one cause), Skullport spies and greater potential threats lay all about them.
PCs do handle real problems, just not all of the real problems.
Eberron doesn't have these types of options as explanations. At least, not coherently.
The real problems, most all of them, in Eberron are of such magnitude - both in terms of raw power and in scope - that the PCs simply cannot be effective.
And people will say, "Oh, but our PCs did X in an Eberron campaign".
To which I reply; "I believe you". And the circumstances that people describe to me seem to be covered under one of two possibilities.
1) That the campaign is/was in fact not run like it is designed with the DM wielding her Heavy-Hand-of-Fiat. Said campaigns require an inordinate amount of time to run because "official" material is not much help, or
2) While any given adventure can seem like it could have world-changing possibilities, in fact nothing the PCs do matter.
If you can keep #2 hidden from players like me, or run Eberron in the way it was not designed to be run, we can all still have fun. :)
I think we have some fundamental gap, but I'm not quite sure where it is.In any but the most open-ended sandbox, there's an element of GM Fiat in setting up the adventure. (Probably in combination with player fiat as well.) If you're playing an AP, the GM (and the players) have chosen to start the campaign in a time and place where certain events are happening that will draw them into the larger adventure. In many cases, that involves some BBEG finally making his move.
The same is true in an Eberron game. Either you set the game when one of the main BBEGs is finally have their plans come to a critical stage or you don't. If you don't, then you deal with other things, life goes on and the horrible evils are only a background worry. If you do, that's likely what the campaign's going to be focused on. Once the starting moves are made and the plans come into the open, the villain can't just stop and wait for the PCs to die. Hundreds of years of planning went to set this up and things are in motion. They can't be put on hold and restarted at a whim. Especially not just because some upstart wannabe heroes have interfered with a few incompetent minions.
I don't understand the "nothing the PCs do matters" argument. That's a matter for the individual campaign, isn't it? How do you want the PCs to matter?
In many cases, if the PCs succeed there won't be much change. If they fail, it'll be catastrophic. Isn't that mattering?