And that's the problem. 9th level wizards and other characters exist, but they are few and far between and you might only meet one of them out of every 500 NPCs you meet.
Whereas we have a band of five of them all walking around together as a super-team. Meaning that they as a group completely overshadow almost every single other character in the setting. Which to me kind of spoils the point of it. Now it's not an insurmountable issue and can be easily handwaved away... but to me it does just lessens the premise of the setting a little bit when you have those 12 to 15 high-level personages that are spread out amongst the dozen or so nations of Khorvaire... PLUS you have 4 to 6 of them all walking around as a group AS though they were the Avengers themselves. And that's only because they are the PCs.
And as far as needing characters that can handle those "high-level threats" in the setting... the only reason those threats like the Quori, Lords of Dust or Lady Vol ARE high-level is because Eberron is a D&D game that uses leveling-up as its reward system that the PCs will eventually reach... so the game HAS to make these threats high-level for if and when the PCs reach those levels too. But I mean if you run the game as an E6... then you wouldn't need those threats to be as high-level as they currently are. One would just de-power most of them so that they still remain as proportionally more powerful than the PCs as they are right now, except the PCs are now 4th, 5th, or 6th level instead. So rather than needing to make a Quori that is a credible threat to a 15th level PC... it only needs to be credible to a 5th.
But like I said, it's not that big a deal and we've all been working with it all along. It's more just the setting's one stubbed toe. But c'est la vie.