The consensus best Legion of Super-Heroes story is "The Great Darkness Saga" of the early 1980s, by Paul Levitz and Keith Giffen. There are many reasons why this is so, but at the moment I want to focus on one that you might not have thought of before.
One of the things that they tell you* is that your language places constraints on the thoughts you can think. Example: in Neal Stephenson's novel Cryptonomicon one of the characters gets addicted to morphine. This doesn't go well for him. At one point one of the other characters starts talking to him about it, trying to help him get a handle on it. I don't have the book in front of me, but what he tells him is something like this: "In English, we would call you a morphine addict. That suggests that your basic nature is as a creature that is addicted to morphine. I prefer how they say it in German, which translates to something like, 'you are morphine-seeky'. The suggestion is that you are still you, but you have the quality of being addicted to morphine."
You get my point? The words and terms that are available to you will influence the course of your thoughts. Here's another example: heat vision. If we were listing superpowers, or if you were designing a superhero, "heat vision" would likely be one of the things that occurred to you as an option. Because you perceive it as a superpower. You have a term for it. But it wasn't always so: look at the early Superman stories and he talks about melting things with "the heat of my X-ray vision". X-ray vision was a superpower; heat vision wasn't even a thing.
Back to the Legion. When you are considering which are the good stories and which are the less good stories, your list will be influenced--determined!--by which stories you can identify as distinct stories, based on which ones have names. And, for the longest time, comic-book stories didn't really have names, mostly. Each individual issue would have its title, but nobody paid much attention to them usually. But multi-issue stories tended not to have names that stuck. This persists today, to some extent, although the titles given to trade paperback collections have some prominence.
Anyway, "The Great Darkness Saga" has a great name, that was used prominently on the covers of the original comics. People who read it got into the habit of thinking of it as a single unit, because they had a term that they could apply to it. So when they were thinking of great Legion stories, or, really, great comics stories in general, it was easy for them to come up with "The Great Darkness Saga".
During Paul Levitz's second run, he didn't do a lot of stories that stood out as units like that. His writing technique had various subplots bubbling along at different stages, and in each issue one of them would rise to the surface and command our attention, and then recede to make room for the next thing, which had been steadily building for the past five issues itself. It's hard to isolate a specific great story in the middle of that. But there was certainly some great stuff in there.
If you ask people now what another great Legion story from that era is, they might name "An Eye for an Eye". Because now they have a title for the story. Before the trade paperback with that title came out, they would have had to refer to it as "the LSV war" or something. They'd be less likely to refer to it, because they were less likely to perceive it as a distinct choice.
Or take "Omen and the Prophet". "Omen and the Prophet" is not that well-regarded, but it does have a title. So someone listing great Legion stories may well find a place for it somewhere down the list, because they do recognize it as a story. But there's lots of other stuff in Levitz's second run that was much better, but doesn't have a title to use as a hook. Or consider "The Lightning Saga"; same deal. "The Lightning Saga" was actually pretty lame in a lot of ways, but it does have a memorable name.
So this is not a slam at "The Great Darkness Saga", which after all really is a great story. It's got an interesting structure, an impressive scope, and some great moments. But one of the most important keys to its reputation has been simply that people knew what to call it.
* "They". You know. Them. The ones who tell you stuff.