So with the current mangling of 5G's ideas in this era, I thought it would be a great time to talk about what could've been with Legion, and likely why it wasn't. Be warned that this isn't fact, nor is it wild theory crafting (as far as I know), but rather an educated guess based off everything we know-- or assume to know-- in and out of the comics. Hopefully there's something here we can discuss.
Bendis' Legion has been something that's been conceptualized for quite a while. It's kind of an open secret that Lee and DiDio basically waited for Bendis to finally make the jump to DC in part because they were offering Legion. If you didn't know, Bendis is a Legion SUPER fan. Along with X-Men, Spider-Man, and other Marvel works, Bendis was regularly following Legion growing up. Alongside his love for Legion, he also really dug DC's Camelot 3000, Herbert's Dune novel, and the indie comic Love and Rockets. All these books he mentioned alongside Legion during an interview for the book talking about how it was a particularly strong and creative time to be reading fiction because all of those books were coming out back to back. That's really where "what could've been" starts-- at Bendis' influences.
As far as I can tell, Bendis' Legion reboot was to be remix of the King Arthur and Camelot myth filtered through the science fiction eye of Dune, and given the emotional interpersonal play of Love and Rockets. Clearly, he read a LOT more books growing up, and those are in there too, but these three seem to really hit upon where he was possibly going with his take.
The first thing I should mention is that early on Bendis insisted that the book was set in the 32nd century, and that it "didn't erase anyone else's Legion runs". If you know Legion, then you know not doing that is functionally impossible due to a number of factors, but Bendis insisted. This is where Camelot 3000 comes in. For those that don't know, Camelot 3000 is the King Arthur myth set in the year 3000. Arthur wakes up in the future after healing from his final battle, and his knights are reincarnated in new bodies (some genders and races don't match up with their old ones). The whole plain is put into motion by Merlin so he can stop Morgan le Fey. The influences in both story and imagery are pretty easy to spot...
Jon is our Arthur. The United Planets is his kingdom/Camelot that he united. The Legion are his knights. But it goes even deeper because Bendis seemed to imply that the original plan was that one of the members of the team-- likely Brainiac-- would remember or have knowledge of the alternate timelines/alternate Legions. This would be how Bendis would make sure that all of the other runs "happened", and also how he would pay homage to the reincarnation idea present in Camelot 3000. This is supported by the fact that you can actually see older continuity Legion members in the visions both Zod and Clark have in Bendis' Superman run. The big stand out tell in the very clear appearance of the member Gates in the image.
This ties into Bendis' take on the Great Darkness Saga. He recently told CBR that he never viewed the Great Darkness as a singular foe or force, but almost a general idea of the oncoming end that the Legion fought back almost spiritually every day. This is supported by the new Guardians of New Oa that Gold Lantern answers to telling him that the Legion itself was the Great Darkness. My theory on this is that it's something of a Many Lives of Moira X situation (but without them knowingly living those lives). By this I mean, the Legion's "we always lose" moment is the fact that in every incarnation no matter how different, they eventually become the Great Darkness. That's why in Clark and Zod's visions of alternate worlds the Legion always comes to kill them. Rather than Mutants vs machines, it's the idea of superheroes vs the dark.
Now, before you say I'm barking up the wrong tree by wildly assuming Bendis was doing Hickman's X-Men in Legion around the same time as it was coming it, let me remind you that the two are very good friends. You can listen to their interviews and see that they like a lot of the same fiction. Hickman, just like Bendis, loved Legion, X-Men, and Dune. And the two have likely talked story in terms of what they'd eventually do if they ever got to Legion (both of their holy grails), so it's no leap to assume that the two went into their respective runs working off some of the same base ideas that they'd talked about in private. I mean, Rucka and Fraction did the same with him even after their books became minis.
The idea seemed to be that Brainiac and the OG three (Lightning Lad, Saturn Girl, and Cosmic Boy) were to act as our "quite council" and likely know the secret of the multiple versions of themselves. Rather than doing what they'd almost always done and brining in Clark Kent from his boyhood, they instead when further into the timeline to get Jon in hopes of that being part of what helps them change their fate as Jon is also supposed to face off against an aspect of the Great Darkness in his present. It's possible the reason Jon is so special to this plan is because due to his journey up till then he'd been left slightly "unglued" from time, and that meant that he could affect things in ways that no one else in his time could. That's in part where the Dune aspect comes in if you know it.
Then we get to the real meat of Legion: who's fucking who.
Bendis made a pretty big deal about the fact that he wanted to have new Legion parings. And I think this was in part due to the alternate timeline stuff. The crown jewel of this is Jon and Saturn Girl. This was to be our Arthur and Guinevere, and if you know anything about Arthurian legend then you know how this ends. We only saw act 1 of what was planned for that romance. Bendis made the romance so spontaneous and "hey, you're hot and I'm hot" in part to play to the college vibe, but also to not treat this as Jon's One True Love...because you know what happens next.
I'm guessing Lightning Lad and Saturn Girl would strike up an affair like Lancelot and Guinevere did behind Arthur's back. This would likely be brought on by them not being able to help but wonder what it was like for them to be together in all those other realties. I also imagine Lightning Lad would've been placed more as Jon's good friend as time went on. There's a very easy to spot Harry Potter influence in Bendis' Legion, and Lightning Lad is very much our Ron (he even has the large number of siblings, and comes from a poor background). Jon's scar not also calls back to Arthur's near fatal scar, but also Harry's.
And if you're under the impression that I'm way off base with all of these theories, please look back at the fact that solicitations were changing drastically and regularly. Just look at what issue 8 was supposed to be
"The United Planets are at war as a new epic begins! The president of the United Planets is unable to maintain peace as Ultra Boy's homeworld of Rimbor and Chameleon Boy's homeworld of Durla declare interplanetary war! With the Legion of Super-Heroes choosing sides and a civil war brewing, will these young heroes need to split into separate teams? Plus, Superboy makes a discovery about the future that will change everything he knows...there is a new Krypton! Find out what happens next in the only book telling you the future of DC Comics every month! "
New Krypton was supposed to be shown 2 issues beforehand, and as far back as issue 3 and 4 Mon-El was supposed to come clean about being Jon's descendent. And either Doctor Fate, Monster Boy, or Gold Lantern were supposed to have a connection to Jon and the 21st century, but that never came about.
And as for who our Mordred and Morgan le Fey were to be? Seems pretty obvious, right? It was Rogol Zaar and the wizard Mordru. As hinted at during his Superman run, Zaar was actually Clark's half brother via Jor-El. If Camelot 3000 comparison holds, then Jor-El likely left him for dead. Zaar was also an "Ultimate" take on the Legion foe Persuader, but no Fatal Five was ever formed or hinted at.
My guess is that eventually Zaar would've been the avatar for the Great Darkness, and he'd have commanded a fatal five armies of alternate Legion incarnations that were infected. Once the new Legion beats back the Darkness they'd likely free the other timelines and give them all happy endings.
Bendis Legion was likely supposed to be much, MUCH longer, and much MUCH more epic in scale. But the shifting of plans for 5G made it impossible to do as intended because so much was clearly leaning on linking closely with the newly formed present day DCU and timeline. The book will unfortunately never get credit it should for how ambitious it was going to be.