I don't know if its been said, but the Citadel and the Relays are an iconic fixture in Mass Effect, they are what Stargates are to the Stargate Franchise, what Jumpgates are to Babylon 5. Without them it's hard to have a series at all. Some would even say that they are more important then ship FTL.
Without Mass Relays, there just is no Mass Effect universe, no economy, no politics, nothing, no sense of unity or orginization. And this is not counting all the destruction the reapers left behind.
Angry Joe points out in his video, that this situation is a "Holocaust nightmare scenario" and I have to agree with that assessment.
As far as those saying that the relays destroyed the star systems, I have seen the videos and discussions, and I have to agree that its different explosion, because in the arrival DLC, its the core that blows up and novas, not the relay, but in the ME3 ending the core energy is clearly shooting off on the space magic beam, why do i say this, because if you look closely, you can see the through the area where the core normally is and see the rings behind it, and the space behind the relay. the center section definitely seems to be "emptying" its contents into the beam just before the relay explodes.
Also, the codex is only up to date as of the last game, it shouldn't be taken as sacrosanct, in ME1 it said that relays couldn't be destroyed, and in ME2, the codex entry says the same thing until you blow up the damn relay and the codex entry updates.
The codex seems to me to be a sort of encyclopedia galactica, of sorts, so its only up to date since the last time it was updated. Considering galactic civilization is pretty much over in either case, no one is around to update the codex, nor anyone around to pick up a copy of the new one.
And If you still believe the energy wave is the relay explosion keep this in mind, those waves go WAAAAAY farther then just the star systems they affect, they spread out to portions of the quadrant, so are you saying that explosion killed those worlds too?
in the vaporize ending, I would say thats true, since the crucible wave vaporized everyone on earth, it stands to reason that the same wave sent through the relays killed everyone in the galaxy. at least in that ending.
I personally am of the belief that the explosion in the end of ME3 was not the same as the arrival relay core explosion, by virtue of the fact that the core wasn't present anymore when it went up.
But ultimately it doesnt matter, since in ANY case, galactic civilization is gone, and travel to anyone's home world is nigh impossible. so in that the ME universe is toast.
And I don't think ANYONE wants to play the ME universe in the future, like thousands of years into the future, it just would seem like a stale flavor at that point.
SO OP I hope that answers your questions, If the ME universe is to be saved the relays are gonna have to be rewritten back into the story. plain and simple.
-AE