1. Take out the Realms Shaking Events that are not adventure modules with PC protagonists.
2. Re-define the Uber-NPC's so they are a bit more spread out in power level. I favor creating about 4 "possible Elminsters" at differing power levels (say 9, 18, 27, and 36), and supply ideas and scenarios appropriate for each. Do the same for the other major NPC's. Different NPC's may be different versions, even ones you think of as associates of each other. For instance, the Seven Sisters may very well be MUCH more powerful than their Little Brother Elminster!
3. Involve the Uber-NPC's directly in the plot only if they're needed. There are more mages in Waterdeep hiring adventurers to do things than just Khelben Blackstaff (who may just be 12th level anyway).
4. Shake up the Evil Organizations and make them nasty, but organize them so lower level PC's have a hope of offending them and staying alive (if only because Team Evil has bigger fish to fry). Speaking of such, allow them to Fry a Big Fish once in a while to help with the Uber NPC problem.
5. Keep the gods, and keep them meddling. Just don't let them meddle in a manner that can be described by game mechanics. They can't drop Bolts from the Blue on people, nor can they convert their favorites into Uber Sock Puppets. However, Tyr coming by and making snarky comments to a PC paladin once in a while has some appeal. One expects such behavior from gods rather than guys like Elminster.
"Why do I have to do that? Why don't you do it yourself, Lathander?"
"Because Bane would come and try to stop me, and us fighting would make a ten-mile hole in the planet. Even Bane doesn't particularly want that, but he will do that to stop me from having my way. I'd kinda prefer just sending you to do it. Neither you nor that guy Bane's sending make ten-mile holes. Also, because I told you to do it, and I'm bigger than you."