@kare_reiko: I think Kino just had to make choices here and there - you can't possibly use every single scene from the novel if you're adapting it into another medium, no matter how much you want to. The pacing would get really choppy for one thing, and some things (like extensive monologues and dialogues, which No. 6 has plenty of) just work way better in a novel than in a comic/anime. And she wasn't given complete freedom either, I doubt it - there's always editors and stuff who supervise and tell you to cut certain things. That's needed, because you develop blind spots for your own work. I think Kino mentioned with some of those pages that she was asked to cut them, actually, so that definitely plays a role. Every writer and creator has to make sacrifices in order to make the story work. It's also entirely possible Kino was given a limited amount of chapters from the get-go, so she had to scrap certain events right from the start to make it all fit, but I don't know about that.
As for the anime... I have no idea. The last volume of the light novels was published as the anime was running, true, but they definitely consulted Asano about the ending before writing it, so I have no idea why they made the choices they did. Part of it is probably interpretation by the anime staff. They emphasized other things than the novels did, and as a result cut out and expanded on different scenes. I don't think No. 6 had a huge budget, so that accounts for the limited amount of episodes, but... I have no idea on why they made some choices, I assume they had to know from the beginning they had only 11 episodes to work with. Why expand episode 1 so much that there's one entire episode dedicated to Shion and Nezumi as twelve year olds, adding events that were later referred to in new scenes they had to add for that purpose (like the sweater)? Why dedicate so much time to Safu's time abroad and then - do that to her character in the end? Why move Rou and his people out of the caves underneath the Facility?
I have so many questions.
Mostly though from what I've seen (not that I'm such an expert), Japanese anime get made while the manga is still running in order to cash in on the success of the manga. In many cases, the anime then overtakes the manga and has to come up with its own storylines - sometimes that works, sometimes it just... doesn't. And other times they take it easier and they stay faithful to the manga as it runs side by side, or the anime gets made once the manga is done. It's definitely a market thing, though. 'This manga is popular right now, let's cash in by making it into an anime!' Or 'This genre/story does well, let's make something almost exactly like it!' I mean, it'd be great if the main goal of an anime was 'let's make a faithful adaptation of this manga/novel and make the fans happy', but it's usually also a money thing. Making a pre-existing series into an anime means you have a guaranteed audience for at least the first couple of episodes, regardless of faithfulness or quality. It's not just a Japan thing - just look at the amount of adaptations Hollywood has been producing since pretty much the very beginning, for example. It's way easier to sell something people are already familiar with than something entirely new.
I don't have any insider information though so I'm just - rambling off what I think might be the case ^^;;;