I'll weigh in here as a big fan of Forgotten Realms, loving the detail and crunchy bits provided in 2nd Ed, but enjoying the 3.0/3.5 rules as the new "way things are run."
I also agree about the Time of Troubles...it sucked hard. Cyric has to be the most retarded villain to come along in quite a while. Adon the vain cleric of Sune was just annoying and useless. Kelemvor was angst-ridden, and Midnight was, well, also annoying!
The plot was jackhammered at us....most of the things stated in earlier posts as being wrong with the story line, I totally agree with... I read the trilogy, and a lot of it gave me that weird look on my face that symbolizes either "Huh? Double-you-tee-eff? This makes no sense!" or "Egad...I've just eaten a turd donut."
And yes, according to my sources at TSR at the time, the Time of Troubles was the plot device used to kick the Realms into Second Edition. Sort of like Crisis on Infinite Earths relaunched many DC titles, only not as well-handled (and Crisis had its problems too, believe me).
Then, to compound the sin of the Troubles, they come out with the Cyrinishad affair in Prince of Lies. Yes! Cyric's gonna arrange for huge-ass armies of dragons and giants to attack Zhentil Keep...THE CENTER OF HIS FAITH...in order to whip his followers into a frenzy of turning to him for their salvation. Oh yeah...THAT makes sense. When he was a mortal, did Cyric burn down an entire house in order to kill a single cockroach?
I'm delighted that Bane returned. Now THERE is an evil god. If Bane can be considered Satan in the Realms, I consider Cyric these days as Wile E Coyote. He's the also-ran who comes up with incredibly stupid schemes which inevitably blow up in his face and make him look stupider than he already is. Of course, in MY running of the Realms, his followers are still dangerous, because they're Chaotic Evil nutjobs imbued with the nutjob god's divine power.
Oh, I definitely incorporated the Time of Troubles in my campaign (because I like doing things by the book...it's a blessing and a curse), although, again like Crisis, it's one of those things that mysteriously becomes harder for the average person to remember ever having happened. And the mortals who ascended to godhood, I depict them as beings who for the most part have forgotten that they were ever whiny, angst-ridden, annoying turds running around the Realms engaging in pointless tasks and soap opera-style plots.