Interesting point, Imruphel.
My Realms has gone through a long history in which it largely followed the official line set by sourcebooks and some novels (which I didn't read, but found their way into the game materials), followed by some serious "FR Year One"-style comic-book retconning. In my original FR campaign, which ran from shortly after the release of the 1e gray box through 3e, I added on pretty much everything that TSR threw at the Realms: The redefinition of NPC objectives, the Avatar trilogy, the rise of a new god of death (a PC rather than Kelemvor, IMC), and the introduction of the Spelljammer and Planescape mechanics as means of defining the universe beyond Faerun. The gods were very real players, thanks in part to my PCs having played through the Avatar modules; they became Mystra's aides and allies, and arch-foes of Cyric and his church. On the one hand, the PCs' enmity was heightened by the fact that they had adventured with the Lord of Lies and he had done all the things a scurrilous party member usually does (taking credit for PC heroics, stealing valuable stuff, verbally abusing other PCs); on the other, the PCs also didn't have as much respect or fear for him as they would have for a "real" god like Bane.
Throughout it all, I certainly tried to tone down what I felt were the over-the-top elements of the Realms: Namely, NPC class levels (which reached a real height in the later days of 2e, what with umpteen 21st+ level wizards running around Westbridge, Longsaddle, Neverwinter, Silverymoon, AND Luskan, among others!). In any case, it wasn't such a big deal, since the players had no idea of how powerful or not anyone else in the setting was. They knew that they (at 21st level) were the biggest guns they knew, except Elminster, Khelben, etc., and that those folk were too busy stopping fiendish invasions, spacefaring marauders, Malaugrym, liches, and others from devastating Faerun for them to ever help out the PCs.
I was never really comfortable with the ToT and certain other offstage events, though, so for subsequent campaigns, I've ditched it. PCs now start in 1356/1357 DR, the gods are remote (so much the their existence is largely unprovable), and the players can reasonably expect that most of the events occuring along the timeline of 1357-1374 DR either may not happen or may happen in a fundamentally different form. That drow ranger everyone keeps talking about may be a roving agent of Vhaeraun trying to muster some goodwill for dark elf males with the surface folk in a scheme to spread the influence of the Masked Lord. Elminster may just be a skilled teller of tales, wise sage, and eccentric, somewhat lecherous old man with a number of good friends and contacts. The Seventh Sister may be closer to Ed Greenwood's original conception: A "Dark Disaster" who is either twisted of body of mind, evil, shunned, or all of the above.
My primary objective is to zero in on the elements that originally attracted me to the Realms: The language, tone, open, rambling feel of the setting, and combination of ancient ruins, scheming mercantile interests and insane wizards that seem to inhabit Ed's stories and Dragon articles.
Mechanically, I'm going with some *seriously* different rules, since I use Iron Heroes. Thus, there's one PC spellcasting class (the mage) and magic is substantially more unpredictable and dangerous than in D&D core rules. "Divine magic" may or may not exist (many clerics can clearly accomplish miracles, but is that the result of Mystra's Art or a direct godly grant?) and the gods' intent is unknown. Large collections of arcane spellcasters certainly are said to exist, but they're in conveniently far-off and semi-legendary places like Thay, Calimshan, Halruaa, or Nimbral.
I also go with a "less is more" approach to races: There are five elven subraces, as in 1e FR (gold, moon, wild, aquatic, drow), mechanically one race of halfling divided into three distinct flavor types (Luiren, lightfoot, ghostwise), gold and shield dwarves, and half-elves and -orcs. That's it. Planetouched and Underdark races may be around, but these are not normally available PC types.
Cosmology is an interesting issue. I used the Great Wheel for my 1e/2e FR games, but I always wanted a more Realms-distinct configuration (this despite the fact that FR has been written from the beginning to fit into the default D&D planar universe). I decided on a Million Spheres cosmology of orbiting Outer Planes all floating in a unified, vast Astral, with Material Planes connected by the Plane of Shadow and material and elemental planes connected by the Ethereal. I allow for planar ascendancy effects a la Eberron, since I love these so much.