I must say that, while I agree that the FR does indeed exaggerate with the number of highly powerful NPCs, what you are pointing out could happen anywhere. It is just natural that if you are a low or mid level adventurer there are going to be people who are more powerful, knowledgeable and experienced than you. It goes with playing in a world that is ''living'', it doesn't spin around the PCs, it has its own forces, factions and people who work for their own goals and interests. And why is it so unbelievable that some of those individuals are not total asses and employ their resources and knowledge to protect what they love?
On the other hand, in a world there are going to be powerful threats, and some of them can't be handled by low or mid level PCs, but it is obvious that -in a ''believable'' (forgive this expression) context- they won't wait until the adventurers are skilled enough to face them in order to act. So (assuming a stereotypical campaign ''save the world/region from X'') the idea to have powerful 'good people' that can stand up to them is not a bad one, they will prevent the big bads from crushing the world, but they won't ever be powerful enough to defeat them, and that's where the PCs come in (after they have gathered enough strength and weakened the big bad organizations, to the point of being able to put an end to them, in a way or another).
You say that it 'diminishes' the work of the PCs, but 1)the good guys can't be everywhere at the same time 2)again, the PCs will be facing threats adequate to their experience, some other NPC will be 'holding' a bigger threat, but they will be struggling against it, needing the PCs' help (assuming that the players want to take part in that, ofc). For example, level 7 PCs could be acting to destroy sharran influence in a region, but they won't ever be able to attack the city of Shade directly. Other people need to keep it in check, in order to prevent them from wiping everything, but their efforts wouldn't be enough and the shades would be slowly but surely advancing their agenda. That until the PCs are able to contribute to a direct attack, taking the spotlight.
Removing so many iconic characters from FR was a bad idea (they and their deities are iconic for a reason), because they could have used a scalpel instead of a sledgehammer. Instead of killing them, they could have introduced an event to weaken them to the point where they would absolutely need the PCs, even at lower levels, because they would be struggling to do what they want to. If Mystra (or any other deity) was that much of a problem, then lessening their influence would have been a way better option than removing them. IMO this would have allowed them to satisfy both old fans and people who couldn't bring themselves to ignore the 'big guns' and wanted them neutralized.
