Yeah, what I mean are branching choices that could change the outcome for some characters at the end of the game, not actual branching storylines. So basically, the overall story will stay the same, and only at the end of a side character’s story there might be a conclusion based on your previous choices. Naturally, it’ll depend on Kirito's ‘prurience level,’ as it needs to be high enough to even unlock those choices.
I mean the Suguha/Sinon scene. It’s a bit hard to describe, but I'll try.
Maybe like this: We don't know what the 'canon' outcome of that competition is because the save file was provided by Fujino. But if we were playing ourselves, the 'canon' outcome would basically depend on our previous choices; for example, if we turned down every choice that involved Sinon, she would naturally have low affection, so the 'canon' outcome would be Suguha winning the competition. This could mean that we missed the flag for an alternate ending for Sinon.
To be clear, I’m not saying it’s true, I just wanted to share my thoughts on this new mechanic and hear what people think about it. But, I mean, at this point, it’s just a technical theory.
As for Klein and Alice, I'm not so sure anymore. It seems to me that Fujino is trying to merge all the stories together so that, for one, every character has the possibility to impact the main plot, and second, they don’t feel disconnected. Before the previous update, Suguha was basically on her own without any real connection to Asuna or Inoda, but with just one scene, she literally became responsible for Asuna’s fall in FOG. There’s also a build-up for a potential Sinon connection to Asuna. So, Alice, who is tied to the council, might also be ‘connected’ with Inoda at some point in the story, which could involve either Kirito or Asuna.