That's fair, I don't disagree with anything you've said — except for Tom Bombadil, I love the flavor he adds to the story.
able to write interesting 3-dimensional female characters
Yeah LotR is a sausage-fest — there is no defending that.
However, this is ultimately a matter of subjectivity, and I don't think I've referred to LotR as the greatest fantasy story. I don't think there can be a 'greatest' of any genre, no more than someone can be 'the greatest' at any sport, skill, or whatever else you can think of. 'Number 1 on the leaderboard' is an ephemeral position and impossible to guage accurately.
In other words, to me I would be more likely to call Harry Potter overrated than LotR, and it isn't like JKR didn't have LotR to pull from. A Song of Ice and Fire, again — very overrated. Despite Martin's attempts to seem like a modern day Tolkien (which he certainly is not).