Lanefan said:
Keep all the gods. Hell, add more.

It's very reminiscent of Greek mythology that way, where the gods are always meddling in peoples' lives.
Some people don't like that. Without polling data or what not, we can't say how many people don't like that, but it's a really common complaint. I think the majority or a large minority of FR fans would like the deities to be less interventionist.
And to whoever doesn't like the idea of a goddess of magic, in a magic-using and pantheistic society, of *course* magic is going to have its own deity...it just makes sense.
There's already a deity of wizards; I don't think magic itself needs its own deity, especially a non-neutral interventionist deity.
Downplay (but don't eliminate) some of the over-used iconic characters e.g. Elminster. Make it clear these characters need never appear in a FR game unless the DM desires otherwise, even if the party has its home base in Shadowdale!
That doesn't really solve the problem. The problem isn't that Khelben or Elminster teleported to the PCs' doorstep and says "do this!" The problem is that anything the PCs do will be outshined by whatever the Chosen or other uber-NPCs are doing. Has anyone played City of the Spider Queen? The drow are trying to summon an evil deity, which is a RSE by itself, and that's clearly beyond the PCs abilities. (They can win, but only because the players know WotC isn't going to write an unbeatable module... hopefully. If the adventurers were really in FR, there's no reason for them not to call upon the Chosen and tell them what's going on, namely that a powerful evil deity is being summoned and they need big guns to handle that. If the Chosen say "sorry, holding reality together today; the old Netheril mages are making all the elf-gates explode" or something along those lines it just shows how too many RSEs result in too many uber NPCs necessary to hold the setting together.)
(By contrast, Eberron does not have ESEs on a regular basis, and can survive with non-epic level good-aligned NPCs.)
That said, play up some of the iconic characters that haven't been seen as much e.g. the Seven Sisters (and who says FR doesn't have strong female characters?).
Lanefan
Not that I've read about all of the Seven Sisters, but with the exception of the Simbul (who is nuts) they're not as powerful as the male characters. Storm walks around in the nude while doing chores like chopping firewood, and this ignores the slightly more reasonable scene of her getting her clothes burnt off (but not her flesh) when hit by powerful fire magic. The drow Chosen has a robe that casts Invisibility
on itself, sort of like how the Invisible Woman in the Fantastic Four movie has the inexplicable ability to make herself invisible but not her clothes (in the comics, she can make herself and her clothes invisible simultaneously, meaning she doesn't strip all the time). It's like reading "the Archimedes Effect".