Hmm, when I was flipping through the LGG (or whatever the big 3e Greyhawk book is called), the pantheon seemed just as big as the FR one - except with weird names. But I like having lots of gods. Not of all them have be in places of importance after all. I use gods that I like, and lock the others down in the basement.
A story line in a campaign setting is bad, IMHO. It's good for the setting to set up lots of potential conflicts and adventure hooks, but not so good to have a meta plot, because those tend to marginalize PC actions, or railroad them.
However, I like FR. I'm buying a setting, I'd like for it to have plenty of detail. It's easier for me to change what I don't like than make up completely new stuff. I don't really have much of a problem integrating stuff into FR. I'm dropping the Banewarrens in Sembia, and modifying one of the cities to fit it, and I've driven the drow out of the Dalelands - since that was our last campaign. It's easy to rip apart or substitute areas of FR that no one ever uses.
Basically, I think it comes down to what we're familar with. I started playing in 2e, and we mostly used FR and Karameikos from Mystara. The pantheon isn't so big when you've used it for awhile. While I'm not an FR expert or have all the old books, I do know the setting pretty well. On the other hand, when I played in a Greyhawk game, I was pretty much lost and confused. I didn't know the gods, geography, history etc. And there wasn't a good place to learn it.
But FR isn't a great place for some storylines. The nation states are pretty weak and far apart. Most important places are city states (Waterdeep, Raven's Bluff, Westgate, etc) or poorly organized collections of them like Sembia or Calimshan. True nation-states like Cormyr and Thay and rare and far apart. Therefore, large scale wars are rather difficult to keep believable, because supply lines could be 1000 miles or something.