I think you're missing the point of Legion/Skynet. What I got from the movie is that no matter how you stop Skynet or Legion or whatever, the AI apocalypse is going to happen regardless. The idea behind it is fine, it's just the execution is what a lot of people have a problem with. In the context with the real world, it makes sense. There is no stopping man's innovation of technology, and man don't want to stop. Eventually there will come a time when that tech comes back and bites us in the ass. That's the point of all this. It's inevitable. They stopped Skynet, and something else took it's place. Just because you stop one company from going down that road, that doesn't mean all technological progress stops, and if progress doesn't stop, it will just lead to this same conclusion again. If Tesla never existed in the real world, it would just be some other company that's going to jumpstart the electric car trend. Even if they stop Legion, they'll delay judgement day by another decade maybe, but in that time, someone else will continue that work to bring humanity and tech to that same peak again where judgement day happens. As long as humans innovate technology, judgement day is unavoidable.
In regards to John, I see his fate thematically tied to Skynet since the first film. The whole idea was to prevent his birth/ascension/survival, etc. so humans don't win. With Skynet finally dead, I wasn't all that surprised that John bites it with one last **** you from Skynet. And now that we have Legion, a new leader is brought up in the form of Dani. So it's not so much that John Connor was pointless, but more so that a John Connor-like role is crucial for humanity's survival, it just doesn't necessarily have to be John Connor who fills it, since it's a different apocalypse from Skynet now. I'd even go as far as to say the ONLY person that really matters is Sarah Connor, because she seems to be fated to be the mother/teacher of whatever new resistance leader that's supposed to rise up to deal with whatever future that ends up happening.
Personally, I feel this is a good way to close out the "trilogy" that started from T1 to T2 and now this. Since judgement day is unavoidable, the best possible course of action to take is, as Sarah puts it, prepare for it. A film about the future battle wouldn't carry much weight to me, aside from seeing the stories that builds up to a certain point where the loop closes, because whether it's Skynet or Legion, the whole idea is that the humans win in the end, that's why the machines wanna change time to kill whoever leader before they can lead them to victory. At the end of the day, judgement day will come, and humans still win in the end. It just comes with the cost of billions of lives before that, and them trying to save those billions just pushes judgement day to a later date, so they might as well just bite the bullet and go through it. And that seems to be what Sarah and Dani are planning to do. It's a nihilistic view, but it makes the most sense to me. So it's a nice send off to the story that started in T1. Again, that's me personally, so feel free to disagree.