One thing I feel that is important to note is that, even in 3e, Eberron was assumed to be lower powered than other settings - even the most powerful spellcaster in the game, Jaela Daran, head of the Silver Flame, is a level 16 cleric, but only while inside the main church, severely limiting her power. No NPC that I'm aware of is stronger than her; I doubt anyone has access to level 9 magic. And there are books that specifically state that Eberron was never designed to use epic levels.
So, in that respect, we're very much talking about a much lower level of magic than FR or Greyhawk, where we have several archmages and epic warriors freely wandering the world. In fact, I would argue that Eberron is very much an ideal setting for many games, in terms of level - most games end around level 11 or so, which is roughly the higher end of much of Eberron as well.
I don't have my books with me, but Eberron do have other powerful NPCs... however, most of them are more likely villains: Lord of Blades, King Kaius III, probably the head of the Inspired, the Lords of Dust...
Anyway, one of Eberron's premises was that characters matter, so they are supposed to be important and grow really powerfull.
Honestly, my biggest gripe with Eberron is the same one I have with most other D&D settings - they're almost all stuck in the Age of Man, with humans dominating so much of the space. How about some variation?
That's probably because most people like to play humans, not only because they are good mechanically, but also for empathy - for the lack of a better word.
But on the other hand Eberron did have a lot of space to play as different races. Goblinoids had their own empire and, even if it has fallen, one important country was basically remincescent of the old empire - you could have a party adventuring there, originating from there, etc.
Eberron had a lot of places for unusual parties and/or campaigns, from the top of mi mind:
* Unding Elves
* Xen'Drik, with tribal Drows
* Sarlona, with psionics, Kalashtar (the psionic race) and others more exotic
* the Mournland could easily make for an Warforged-only campaign
Not to mention the importance of the Dragonmarked Houses. Yeah, most of them were human, but we had a fair share of others in interesting roles: Sivis gnomes with comunication and transport, Kundarak dwarves with banking, Tharashk with detective half-orcs...
Even though humans had a lot of space, most other races had a fair share of the spotlight IMHO. Heck, even half-orcs who were "sons of rape" in basic 3.5e had a better place in the world.
Most of all, those things that seem prety puch like a collection of weired stuff really had a background, a reason to be there, history and lore that made them credible and interesting...
Did I say that I miss Eberron ?