In Scott Pilgrim vs. The World at first I thought Nega-Scott turning out to be pretty nice was just meant to be a joke. Later I realized that, if Nega-Scott is the negative version of Scott, and Nega-Scott is an okay guy, what does that say about Scott?
Scott is not that great a guy in general. He grows a lot as a character, but he still was kind of a tool, though not evil and had redeeming qualities. Like a real person, or more specifically, like a real barely out of college male, he is somewhere in between good and bad. Thus his negative version would likely be that way as well. In fact it is likely due to the fact that he wasn't particularly good or evil that he avoided having to fight his "evil" double. Being well rounded avoids needless conflict.
That, or the fact that Scott is neutral. What is the opposite of Neutral? Also neutral (if you class good as the opposite of bad in this case)
Possibly meant as Rule of Symbolism. Some believe that in order to overcome our dark sides, we must make peace with it rather than constantly fight against it (i.e. acknowledge that we have this aspect to ourselves and take steps to avoid indulging in things we shouldn't rather than continually fight against that part of ourselves in hopes of destroying it completely).
Scott is not only neutral, he's a zero, and negative zero is just a zero as well.
The deleted scenes show Nega Scott appearing whenever Scott is wishy-washy or selfish in his relationships, first when he runs away instead of explaining his past relationship with Knives to Ramona, then when he lashes out and is a jerk to Ramona over the Evil Exes. By the time he's expected to fight Nega Scott though? He's realized the error of his ways, taken responsibility for his actions, and apologized to both Knives and Ramona. Considering how the movie focuses on themes of relationships, it's not a leap that Nega Scott represents Scott's inability to commit instead of his overall negative qualities and that beginning to grow into a more mature partner renders Nega Scott no longer dangerous.
The scene where Stephen Stills remarks that "Girlfriends are no longer allowed at band practice" initially plays as if he doesn't want the new girlfriend of the band's barely competent bass player distracting him or his girlfriend hanging around making bitchy comments, and his glaring at Ramona when she arrives is him being upset that his new rule didn't even last 5 minutes... Until you realize that in the books, Stephen Stills comes out as gay in the last volume Mark Webber (who played Stills) was one of the few people who knew this prior to the book's release. With that in mind, watch Stills in the time between his initial remark & Ramona's arrival. He's checking out Scott.
Notice how when Matthew Patel appears, the conflict with the League of Evil Exes becomes so prominent, it takes over the film & there's only mere minutes between fights? It's because we're not watching a film with video game influences, we're watching a cinematic video game. The fights with the Evil Exes are the levels, and everything in between is a cutscene.
When Scott dies in his fight with Gideon, his extra life resurrects him not after his fight with the Kataynagi Twins (when he got the Extra Life) but after Ramona leaves him & he quits Sex Bob-Omb, because that was a cutscene. Everything that follows & that Scott does better the second time is "Gameplay".
Plus the scene with Ramona telling Scott about the computer chip on her neck after Scott dies & before his resurrection is reminiscent of certain games giving the player advice after they just died.
We get to see all of the fights with the Evil Exes, but we don't see what happens with Nega-Scott, who just... appears. Why? It's because he's a bonus boss who doesn't affect the outcome of the game.
ALL the hidden numbers in the evil ex scenes, especially the not-so-obvious ones. Lucas Lee points with TWO fingers. G for Gideon is the SEVENTH letter in the alphabet. Wallace calls Matthew "That ONE guy..."
Lucas also comes out of a trailer marked with a 2. And while Todd wearing a 3 on his shirt is less than subtle, he also tries to get out of having his "vegan powers" taken away by asking if he got a three strikes policy.
Also, in the Katayanagis fight, the sixth and fifth exes are standing from left to right respectively, while usually numbers go left to right as they get higher. This is because in Japan, people read from right to left.
Scott also wears a "Zero" t-shirt throughout the film...
Not to mention he drinks Coke Zero, is called a zero, etc.
Nega-Scott's arrival at the end of the movie happens with absolutely no explanation, until you remember that Ramona dumped Scott when Gideon came back. In other words, Scott is facing Ramona's eighth evil ex, himself. However, by not backing down from the fight, Scott is essentially acknowledging all of his dickish behavior and showing that he's ready to make up for it. In the process, he proves that he wasn't (as Ramona put it) just another evil ex waiting to happen, and Nega-Scott is neutralized, letting them avoid a fight altogether.
If you take the comic book's Nega-Scott into consideration (i.e. the negative impact of all of Scott's decisions.) it makes sense. At this point in the movie Scott has acknowledged his mistakes and grown past them. He literally made peace with his dark past.
When Scott has his second dream about Ramona, he's walking through what appears to be a high school — rows of lockers, tiled floor pattern. Where did he first see Ramona? A library. What did he say libraries remind him of? Grade school.
When Sex Bob-Omb is facing the Katayanagi Twins and summons the giant yeti thing, Scott's eyes are the same glowing green as the yeti's. He's controlling it, most likely through how pissed he is about Gideon.
Lucas Lee isn't that bad a guy in the movie, and is openly friendly toward Scott in the comic. While Scott still fights him before tricking him into killing himself, the unantagonistic duel to the death comes off as unusual in the storyline. It's an early hint that Scott's an Unreliable Narrator, and he himself isn't able to reconcile killing Lee.
So Gideon gets Ramona back with his limo playing "Under My Thumb", a song about a overly-controlling guy getting his girl back and not only describes the gist of Gideon but also foreshadows the evil mind control chip with "The way she does just what she's told/Down to me, the change has come/She's under my thumb".
Todd's entire vegan style, and thus powers, are made as a Take That toward real life vegans (and hipsters in general) who think of themselves as being above other people. Envy not only literally says "being vegan just makes you better than others", but he's also made to be essentially overpowered (reads minds, flings Scott around with psychic powers, walks through bricks walls effortlessly, etc), even more so than the other exes at least in theory. Basically a sarcastic "Yeah, look how cool vegans are!" while also making him an idiot and becoming a shamed, quivering mess (right before he dies) when his vegan powers are taken away, which in itself doubles as saying those same egotistical vegans would have nothing to brag about if they weren't vegan.
In Scott Pilgrim vs. The World, Scott is basically a serial killer, except everybody he kills turns into coins. What if the movie took place in the real universe? Lucas Lee would have his skull cracked open on the sidewalk in the skateboarding accident. Gideon would have his head kicked off his body. Roxy would die because of a heart attack caused by the intensity of her orgasm.
How is he a serial killer? These people are part of a conspiracy trying to kill him.
Well, he murdered several people in a row. That makes him a serial killer. It might be that it was in self-defense, but people like Todd and Gideon were no longer threats to him. Plus, he was setting out to kill all of them anyways, in order to date Ramona.
To quote Millennium's Frank Black, that would make him a spree killer, not a serial killer.
A few of the deaths (someone orgasming to death and someone being goaded into a risky and ultimately lethal stunt) might possibly still count as crimes but they don't really fit the bill of Scott killing them.
Now, remember that the video game imagery and outlandish histories are implied heavily in the comic to just be Scott's way of not having to deal with reality (the movie glosses over this, but that punching a guy so hard he saw the curvature of the Earth thing? He believed that in the comic, until he fought Nega-Scott and realized it was a lie he'd told himself to cover for beating Kim's boyfriend). He killed people, and imagined that they burst into coins.
In an alternate ending, this was the true intention of the film.
There's a precedent in the movie for people who die coming back to life. And Scott even hears Gideon's voice after he's gone. Its implied that Death Is Cheap for everyone in the Pilgrimverse.
Also, during his first fight with an "Evil Ex", he accidentally kills his competition. It's brushed over, and you may miss it if you don't pay attention. Not only does he kill someone who's not even part of the conflict, really, one of them is a girl who looks to be about 12.
Scott doesn't kill them, he just dodges the fireball that would've killed him, and Word of God is apparently that they respawned. You can see them spectating a couple of minutes later.
It's implied that Matthew Patel sent Scott the email regarding the impending fight as a result of the mass text sent out by Stacey. Congrats, you nearly got your brother killed a few times....