Some of the reasons I've heard are pretty ridiculous "I don't like Elminster", seems to be the funniest, just because it's so easy to just not use a specific NPC if you don't like them, and because they come up so rarely anyways, unless the DM builds his campaign specifically to make use of them.
Insulting other peoples' opinions isn't a good way to generate discussion.
Sure, you can just write out Elminster, but then you're making a big change to the Realms.
For people here.
1. Do you avoid Forgotten Realms products?
Some of the novels are good. I avoid any with Chosen of Mystra in them.
2. Do you like either Pre or Post spellplague only, and if so which one and why?
Both have their charms.
3. What Don't you like about Forgotten Realms?
Too many high-powered magical good-aligned NPCs with non-specified but ridiculous powers. Not just magical ones either. They're all incredibly intelligent and charismatic (not surprising, the authors have months to write a novel), have vast resources that would make S.H.I.E.L.D. jealous and run their own spy networks. They all know ancient lore that no one else would know. The good guys are so "overpowered" (not (just) in combat terms*) the bad guys never stand a chance. Sure they can make mistakes, but never the same kind the PCs make.
And not only is the god of magic a main character in the old setting, but she's
good-aligned! (Dragonlance, at least, did this right by having three of them, one of each alignment.)
Sometimes the CoM novels seems like bad James Bond parody novels, but only worse; Bond can't teleport, and he still has limitations. And if something bad happens to him, Elminster's Evasion or a goddess will not literally save his life.
So in short, novels featuring important good-aligned characters damaged the setting. You can throw them out, but then it's not really the Realms.
*In fact, in 3e the Chosen of Mystra were wimps, ruleswise, compared to their 2e counterparts, but that's in part because people tried to convert them as "closely" as possible. (They all have insanely high stats that they "rolled" in 2e, not counting the Constitution boost, but no stat-boosting items, and their item selections usually suck, too.) But their rules combat power isn't the real issue.
I should point out I'm only complaining about a few subseries or authors, it's just too bad the Elminster and Friends subseries is one of the most important. (Also, I will complain endlessly about Elaine Cunningham. Drow shouldn't get to slap Lolth in the face and get away with it.) The six-part drow "Dissolution" series was not only pretty well-written, but the drow
were actually evil! (Well, most of them. None were good.) And I really liked the Erevis Cale trilogy that I read, and several others too.