Hoo boy, am I gonna draw some flak for this...
Eberron.
And not for the obvious reasons. I have no beef with Warforged. I like the dragonmarks, I like Sharn, and I love what they did with aerenal elves and the dino-riding halflings. I like the magical trains. In fact, I like all of the "trappings" - the weird little things that add spice to the world.
The problem is: The Big Bad Evils are deadly dull.
Compare with other TSR campaign worlds... Greyhawk has Iuz and the Scarlet Brotherhood. Ravenloft has Strahd and Azalin. Planescape has the Abyssal Lords and the Lords of the Nine. The Realms have the Zhentarim and the Red Wizards. Birthright has the Gorgon. Spelljammer has the illithids and the neogi. Krynn has the dragon highlords.
Now, sure, all of those campaign settings have many other big bads (Rary the Traitor, Vecna, yugoloths, Cult of the Dragon, etc, etc, etc), but there are a couple of groups which are marquee villains. You have instantly recognizable protagonists with clear motivations. They have history and "weight".
I don't think Eberron has done enough to establish 1 or 2 "signature" Big Bad Evils. You've got (in no particular order, and I'm no Eberron expert): the Lords of Dust, Blood of Vol, Shadow in the Flame, undead from Kaarnath, scorpion-drow, abominations from Xoriat, the Lord of Blades, weird psionic mind-monsters... it's all over the place.
That's good, in that it creates immense flexibility for DMs and adventures. But I think it's also bad in that, for a newcomer at least, there seem to be a hundred different evil groups out there. And (deep breath) few of them are particularly interesting.
- The drow are like other drow, but... uhh... they have scorpions instead of spiders. And their driders are sort of... drorpions. And they're... uhh... patriachal instead of matriachal.
- We've got warforged so... let's have a bad warforged who wants to conquer the world in the name of the warforged.
- Demons and devils have been used so much in the past (chained up, but striving to break free in Greyhawk, Realms, etc), so let's use rakshasas for a change. They're pretty close to fiends anyway.
- Let's randomly create some uber-aberrations to create and master all the other aberrations. Let's diminish the mystique and horror that already surrounds mind flayers and aboleth by making them merely experimental creations of the mighty... uhh... daelkyr. Who you've never heard of before.
There do seem to be some truly unqiue and fascinating evil groups. The Blood of Vol (from what I've seen of it as a player) is a cult of death-worshipping elves who are fascinated with immortality. That's *interesting* to me - I haven't seen it in other campaign worlds. The concept of the Shadow in the Flame is also interesting. Again, frow what little I've seen as a player, it seems to be a hidden heretical sub-cult within an overtly Lawful Good religion. Very different.
I think Eberron would be a more interesting world if they focused heavily on (say) two of the more interesting evil groups and really promoted them as a deadly threat. Keep the rest very loosely defined as options for individual DMs to explore further.
On a side-note, I also find the nations themselves kind of dull. As a player (who doesn't own any of the Eberron supplements) I can only really identify Kaarnath as unique: it's the the slightly-crazy, militaristic undead nation. The others all seem to be pretty generic "fantasy nations" with the unusual range of slight cultural differences.
Now why I do realize everyone has their right to their own opinions, I have to respectfully disagree.
Eberron is full of great Villains - even the leaders of every country is a potential huge villain for a campaign, depending on how the campaign goes.
Some of the big bads you've identified aren't so bad really - The blood of Vol is an Unaligned religion in itself, practiced by many regular persons, especially in the nation of Karnnath. The bad guys in it are most of the High up Clergy, who are mostly Evil and/or Undead; and of course Vol herself - who to me is a Big Bad for the setting, she caused a huge ongoing war between the Elven nations and the Dragons to end temporarily to destroy her Clan just by being born as a Half-Green Dragon-Elf. She's got a huge organization of flunkies called the Emerald Claw (named after her father) and has lots of cool things going on, hooks into Karnnath, stormreach etc.
One of the things you missed for villains - or at least the point of - is the Dreaming Dark. These guys are great villains to me, they are working behind the scenes everywhere, they are willing to bide their time, working slowly towards their goals. Anyone you meet, or even party members could be mind-seeded. Their minds are completely alien to humanity, and they can infect your dreams, turning them to nightmares. The scary/weird Quori form is only a minor part of them. The huge monolithic culture they control, and behind the scenes chicanery is the important parts of them to me.
The Daelkyr serve as great enemies for Primal Heroes, and good end bosses for Aberration thick campaigns, they aren't really supposed to be marquee for the setting, just a way to get Cult plots going.
Lords of Dust/Overlords/Rakashas - These are all here not to be marquee evils for the setting (though can be easily focused on for single campaigns, and be great) - they are more for the general demon/devil type plots you would see in any setting, and would be wrong to have missing in the setting... Rakashas are not replacing Demons, they are just being granted equal time with them, as they are just as cool.
The Lord of Blades - this guy is a semi-marquee guy in my mind - But less in the basics of him being a Warforged extremist but more in the possibilities of him actually being something else.... Was he once Aeren d'Cannith? Did he Kill him? Or is he Bulwark, once friend of the King of Brelend? Is he secretly funded by Merix d'Cannith in Sharn? Did he cause the mourning? Something Else completely? Its completely up to you to decide.
And that is the point of Eberron's villains - you (the DM) decide. Who is going to be the marquee villain of YOUR game, decide their motivation. Or come up with a general plot, and figure out the villain that fits best for it.
As for the other stuff, yeah some of the nations are a little generic - Breland: land of heroes and (magical) industy; Thrane: LG theocracy; Aundair: Romance/Courtly/Chivalry in a land of Magic; Karnnath: Warlords and Undead troops; Eldeen Reaches: Druid land!; Droaam: Nation of Monsters trying to fit in with civilization; Darguun: Nation of Goblinoids trying to stay together despite themselves and stay in Society; Talenta Plains: Nomadic halflings on dinosaurs; Mror Holds: Dwarf-land; Q'barra: Jungle Frontier nation trying to reclaim past glories; Llhazar Principalities: Semi-Independant city-state islands, each one different & PIRATES!; Shadow Marches: Marshy lands controlled by Orcs and Humans living in (semi) harmony
Now of those listed there... the only ones that seem really generic are: Thrane, the Eldeen Reaches, the Mror Holds and maaaybe Aundair. The other nations are much more alive and interesting - to me at least. And the boring nations still have lots of cool things to do there, other than the Mror Holds. Can't ever really see myself setting something there.
I could keep going, but I really really love the setting, in my view it is really well designed, able to fit many many different types of campaigns, and it meant to be PLAYED rather than just read about.
Thats one of my biggest problems with the Forgotten Realms really, 4E helped it a lot in that regard, but I still couldn't wade through the Campaign setting.