Loved/WMG

The narrative is about a strained romantic relationship.
May as well get this one out of the way first, right? Anyway, it goes as such: When you choose disobedient options, the tone gets increasingly harsh and derogatory, and picking "go" during the final choice results in the Voice insisting that it really had loved you throughout the verbal abuse. I take this to mean that the player and the Voice are in a relationship, which had grown strained over time or through stressful events; disobeying the Voice's orders is the player refusing to work on the relationship, instead doing whatever they like and causing their partner to become more and more bitter towards them. Of course, many people will stay in a relationship they'd unhappy with even after it goes bad, so when the player finally makes the choice to leave the Voice abruptly switches gears, trying to get the player to stay, and finishes with 'I always loved you.' The abrupt end to the Disobedient route is the player cutting their ties with the Voice and leaving the relationship.

When you choose obedient options, however, the player is being conciliatory towards their partners; obeying the directions equals jumping through hoops to please the other, even when the choices are counter-intuitive (Don't touch the statue) or outright destructive (Throw yourself into the barbs). Yet these choices are also pleasing the partner, who thus becomes calmer as they gain control of the relationship; choosing to 'stay' indicates that the relationship is at least functional again, causing the Voice to reward the player with acknowledgment (i.e. Choosing 'boy' gets you "No, you're a man.") and praise ('I'm so happy to have you'). The end of the Obedient route has a more 'traditional' platforming style, complete with coin, representing the player's reward - a 'normal' relationship - for having pleased their partner.

Of course, neither option is entirely perfect: The colorful pixels when disobeying represent the chaos and disorientation that comes from strife in your relationship, becoming severe the more you disobey because attempting to break from a long-time relationship is exceptionally difficult. And while obeying nets you an easier time (no disorienting pixels), it becomes if anything even more stark, blank, and inorganic then before, representing how the relationship may be fine on the surface but is - at least on the player's part - lifeless, requiring them to put so much effort into pleasing their partner that there's no real love or emotion (color) involved.
 * As I see it, the disobey option is perfect. The black path the player follows would be the relationship, and with each act of disobedience, the black-and-white (as you put it, lifeless) path gets broken by colourful blocks, which is not you struggling to break the relationship, but the relationship breaking by itself once you don't start blindly following the bad advices (or, well, start disobeying good advices because sure why not). The player is not struggling to break the relationship, going further to the right is trying to go on with it, but the relationship(path) is breaking itself because the player is making his own decisions. Thus following the relationship becomes harder, since I'm not even sure where I am going with this.
 * As the above illustrates, even the 'good' option - ending the relationship - isn't perfect: The player careens towards the other end of the spectrum, doing exactly the opposite of what the Voice instructs even if it hurts (kills/shatters) the player in the process. By following the Disobedient method, you become as defined by your opposition to the Voice as you were by obedience to it; perhaps the Voice/your lover really does intend the best for you, and you're throwing it back in their face. Perhaps your attempts to prove that you neither want nor need them drives you to dangerous behavior, as you justify it by saying "Well, I'm not gonna do what you want me to do!" While following one's own path is important, disregarding good advice just because of who's giving it is throwing the baby out with the bathwater: The key is to follow the good advice and disregard the bad, allowing a clean break without too much hurt between you and allowing you-the-player to achieve the Leave ending without plunging wholesale into unnecessary chaos.

The game follows a stalker/pedophile/etc... and the boy/girl he/she kidnapped
Similar to the above, but rather than just a strained relationship, the main character is a victim of the unseen speaker. The kidnapper is trying to get the MC (henceforth to be referred to as "you") to be obedient, and when you disobey he hurts you, binds you, gags, you, etc... which is why the world becomes more distorted - you lose methods of seeing it. But the final levels of the game, notably somewhat harder than the rest of it, are not just mental metaphors, but actually escaping the kidnapper (still semi-metaphorically, but for the most part literally). Thus, once it's too late for him/her to stop you, he/she makes one last attempt to get you to come back saying "I always loved you." Staying means succumbing to Stockholm Syndrome or simply giving up and relenting to your captor. The clarity that comes with obeying is becoming more used to your surroundings - it becomes your "home."

The game follows an abusive parent and his/her child i.e. you
Perhaps it's all one long drunken rant or several instances of abuse, but your unseen tormentor is your mother or father, verbally and physically abusing you when you disobey. You leave, saying enough is enough with the abuse and the fear and the distortion and pain, or you stay, and try and pacify your abusive parent rather than live a free life. the tormentor is not lying when they say they always loved you as a parent does, but he/she failed to act appropriately as one. The pixelation and discoloration is both physical effects of abuse as well as chaos and fear of a child turning away from a parent. The clarification comes with identifying your environment more as you grow up and become used to it - eventually completely coming to terms with it and remaining loyal to the parent despite his/her actions.

The narrative resembles that of a drill instructor and recruit.
I got the sense that the voice resembled that of a drill instructor. They begin by degrading you and telling you that you're a child of the opposite gender, however, if you continue to obey and reach the goal, you're eventually praised as an adult of the gender you choose. In addition, while they were harsh, their advice was good and made later puzzles easier, even if earlier puzzles were harder as a result. This fact also gives credibility to their claims that they loved the player all along. I'm not implying that the voice is literally a drill instructor, but that the relationship is one where the voice "breaks you down" and "builds you back up".
 * Interesting... But then what about the ending where you 'leave' the voice?
 * I played through the "obey" route the first time, so that's the impression I got. I didn't really take the other routes into consideration.

The game is an S&M session between GLaDOS and Totoro

 * Sweet Zombie Jesus, my mental eyes! The Goggles Do Nothing!

The Voice Is The Voice Of God
Demands obedience, claims to love you, gives no rewards for obedience, but gives punishments and insults for even the slightest disobedience? Sounds like god to me...
 * No rewards? You are finally considered a man/woman at the obedient end, and could possibly be off to a land of happy-happy-rainbow-lollypops you just don't see. Or to an eternity of torment.

You are dying, and the voice is a loved one trying to bring you back.
You're delusional or in a coma. The harsh things the voice is saying to you is just your interpretation. Even the barbs you have to throw yourself on could be considered another gateway back to reality. In the end, you either return to life, die, or are trapped in a coma forever. Also, the coloured squares could be you losing your grasp on reality, while the other branch could be you regaining it.

This is occuring in the world of Azumanga Daioh (according to the darker WMGs for it).
Because the avatar looks like Chiyo-chichi, Bringer of Madness.

You were working at a job all along
If you're obedient and excited, your reward is... a coin. If you're disobedient and afraid, you get fired, or quit. Failing to obey has the side effect that you don't understand what you're supposed to accomplish. So the world goes all blocky. Your boss is a jerk, but you must really want that job, to go through this Training From Hell.