The whole discovery point system and the way it ties into getting the good ending is rather silly. Why should Artyom be considered inquisitive and willing to understand the Dark Ones for playing his own guitar, or finding a fallen body in an out-of-the-way location? It would make more sense if it was just actual encounters with the Dark Ones that counted towards the ending scenarios.
Pissed me off too, though possible justifications would be that Artyom's 'moral points' are looked at in terms of both Artyom's own realisations(the horrors of war, seeing enemy soldiers talk about their families etc.) as well as the Dark One's view of him. Stuff like playing guitar and exploring could be seen as thinking outside of the box which is why the Dark Ones would further try to reach out to him. Remember the playground flashback in which if you start shooting the voices say 'He does not understand. He only wants to kill.'? A player who does not explore is by extension dead-set on his objective of killing the Dark Ones, which means that in the finale they'll try to stop you by any means(killing you), rather than trying to reason with you 'till the very end.
The problem with this logic: if you explore enough to get the option of sparing the Dark Ones, they still try to kill you in the end anyway, and they never make any clear statements of desiring peace until the very end. It's awfully convenient that they try to kill Artyom, and only after that do they suddenly start explicitly saying that they want peace. Before that, all their speeches are along the lines of "Why would he want to hurt poor innocent us?", conveniently overlooking the attacks on Exhibition station that started Artyom on his mission in the first place.
Gameplay and Story Segregation. In the novels, the Dark Ones always wanted peace (and Artyom was their 'chosen one', because he was the first to have contact with them, when he was a child); in the video game, for the sake of a more developed climax, the Dark Ones are depicted as being far more desperate - and less inclined to share with Artyom their original intentions. Furthermore, even though they have some sort of Hive Mind, as the Hive Mind trope points out, this does not necessarily mean they are incapable of exhibiting individuality. The one that pursues him up the tower with the intent to kill Artyom could be acting on its own, and the others are unable (or unwilling, being pacifists) to stop it.
This is exactly it. It isn't Artyom making a decision, it's Artyom being judged and reacted to accordingly. If you explore, experiment, get in touch with the softer things, etc, then the Dark Ones will see you as someone who is willing to see certain things in a different light, and that you could consider the surface worth nurturing. If you play it like a regular FPS, and thus a murderous nut who doesn't take in the world at large, then you're quite rightly seen as aggressive and tetchy and warmongering - something the Dark Ones don't want.
Artyom never left Exhibition station after being saved by his stepfather. He doesn't know a thing about the world outside VDNKh. You poke around corners and listen to dialogues - you learn how this new world works, you get to actually MAKE A DECISION based on your knowledge - Kill dark ones or save them. There is also neither GOOD nor BAD ending, both are just alternatives to each other, Grey and Gray Morality, so to speak.
It's basically based around Khan's quote "Try to get a better understanding of things before you make your judgement".
Why does Artyom narrate all the loading screens but becomes a complete mute as soon as anyone attempts to talk to him in game?
He doesn't really narrate, he writes mémoires on his typewriter that you read in your head with his voice. He is also the Heroic Mime.
Okay how the hell does he get off that tower?
Fancy parkour that would be too fiddly to show in a first person perspective.