@Justice League
First, it's not
just the Chosen of Mystra. They are simply a lightning rod for criticism. There are lots of these powerful, invested NPCs who have abilities outside the reach of PCs (high levels, unique abilities, artifacts, etc.). This includes epic levels, as well. Saying that you could have the same abilities as Elminster if you, too, were 36th level is operationally equivalent, in over 90% of cases, as saying you can't have those abilities.
Second, I'm not an "expert" about the Forgotten Realms. But, I think I could be forgiven in thinking that, as far as 3rd Edition D&D is concerned, they really ARE the Justice League:
While in the ELH it says that "in his advanced age he now prefers to work through younger and more vigorous heroes rather than moving directly against his foes." It also states:
During the Time of Troubles, he saved Toril ...
Elminster ... delights in acts of whimsy, helping the needy and lovelorn, and dispensing poetic justice to those who deserve it. He has a heart of gold, and a deep need to bring tyrannical, pompous, and cruel persons low ... nothing awes him or leaves him much afraid.
The emphasized passages read very much like a hero's job description. The other stuff is just kind of fanboyish Mary Sue stuff. Indeed, if you deleted "Elminster" from his entire description in ELH and replaced it w/ "Alan Scott" (the original Green Lantern, now an active elder statesman hero in the DC Universe), one would be hard-pressed to tell the difference. Probably the same thing could be said about Martian Manhunter, both major, active members of the Justice League, though Scott's adventures have mostly been part of the Justice Society of American in recent years.
But, Elminster is actually kind of a bad example. Let's take Storm Silverhand, 32nd level Chosen of Mystra:
The famous Bard of Shadowdale [note: what? They both live in Shadowdale? Damn, that is one safe Dale ...] ... spends much time ... protecting Shadowdale against its foes ... Storm's grim, get-even temper leads her to arrange 'poetic justice' [note: does Mystra choose her people just based on their ability to use irony?] for swindlers, thieves, arsonists and vandals, and tyrants -- and she'll combat such foes w/ no through for her personal safety ... She's also a personal favorite of the goddess Mystra, who several times whisked her away from certain death.
Again, I think a reader could be forgiven for the thought that Storm really was a hero. I mean, she really does read like one, right? Now, maybe the Realms writers walk all this back somewhere. I don't know. But, they really do sound like a bunch of meddlesome do-gooding DMPCs. Storm even has explicit plot protection, which is pretty funny for a high-level NPC w/ the Chosen of Mystra template, and whose best friends are the most powerful mages in Toril.
Further, you'll notice a lack of any of the descriptions of the Chosen of Mystra being withdrawn from the world (all there is one sentence to that effect in Elminster's description), nor is there any mention of them safeguarding magic, or anything to that effect. Indeed, Khelben is a "grim, inflexible proponent of law and order." Alustriel is moved to action by injustice and intolerance. The closest would seem to be the Symbul, who is concerned w/ mastering magic and single-handedly destroying armies, which puts your successes in perspective. Furthermore, it explicitly states that "It's seemingly impossible to ... overload [Alustriel's] concentration on multiple matters at once ... Her wits and experience enable her to better anticipate future events in the North than almost anyone else in Faerun." So, it might take a big excuse to move this CR 28 spellcaster off the board if you were tromping around the North. Or, the event is beneath her notice.
Maybe there's some passage to the opposite somewhere, but in this place where they collected a lot of these NPCs, though not all of them, in one place they really read like the Justice League. Or, at least, that impression is certainly not obviously wrong in any regard. And, I'd beg people to stop acting like only a moron could read them that way.