Both branches of the initial route split start with small ones. Walter is obviously relieved to have you join him, and Jonathan cries if you choose to side with him. Having people at K's Tavern comment on how good it is to see you and your partner getting along makes this better or worse depending on where you end up on the alignment chart and your feelings about the alignment heroes.
Even though the place is full of horrificrevelations, one of the gas-masked workers who works with the kids in the Reverse Hills Building legitimately loves working with them, which is...oddly heartwarming.
The entire Neutral route can feel like one. First, Stephen congratulates the player for rejecting the temptations of the other routes, choosing instead "a world without bias." Then, upon your return to Tokyo, Isabeau is so relieved to have you back safe and sound that she has to fight to not burst into tears. Later, you're tasked with bringing "hope" to Tokyo, which you do by completing challenge quests. As you complete specific requests and your overall ranking with the Hunter's Association goes up, NPC dialogue changes to reflect the growing hope your actions are bringing to Tokyo. When you finally take the top rank, you embark on a "victory lap" across Tokyo since you've become so famous and beloved by the populace that very presence inspires hope in the people. It's incredibly satisfying, and a great way to get pumped to kick the crap out of the angels and demons threatening the city.
How you shut up the Issachar-shaped White in the Neutral Path. In the Chaos Path, he taunts you by reminding you of Blasted Tokyo and Jonathan's desire for a peaceful, ordered world. You proceed to deliberately forget about Jonathan, weakening the White so he can't use the memories against you. Likewise, in Law, he reminds you of Infernal Tokyo and Walter's wish for a free world of perpetual change. Again, you forget about Walter to give the finger to the monster. In Neutral, he invokes the memory of both. You proceed to silence the thing by refusing to forget either.
The final Neutral quest, "Returning to Normal", is personally named by Burroughs. This is a goddess who's been reduced to Mission Control for the past 1400 years and she knows that regaining her godhood is finally within reach.
Also, after you defeat Merkabah and Lucifer, when you return to Café Florida, you find Commander Hope standing outside, clearly proud of your accomplishments. Inside, you find Isabeau, Fujiwara, Skins, K, and Hugo relaxing while talking about plans for the future. Burroughs even notes that the atmosphere seems to have changed to something that wasn't seen in either Mikado or Tokyo yet. This culminates in the ultimate goal of having the true form of Masakado tear off the Firmament, finally bringing daylight back to Tokyo after 25 years. And at the end, right before the credits roll, Flynn encounters the girl again who transforms into the Goddess and gives him a simple yet nice 'thanks' when the screen cuts to black.
Reading manga with Isabeau in the neutral path. There's no real reason for the scene to be there, but it's happy enough, and satisfying that despite Lilith's earlier claim about it, Isabeau did indeed find the conclusion to Oscars and her companion's story.
Some of the demons in the Neutral path will even root for you! The Four Devas tell you to keep going down the path you chose, regardless. Amaterasu gives you the Torifune's Shawl; she then says that she will return with the Amatsu to help rebuild Tokyo.
It's twisted, but there's something kind of touching about the Chaos ending. Lucifer mentioned earlier that through him, Walter is with them. He wasn't kidding: there was no way he would know about the scene with Flynn, Walter and Jonathan on the top of the castle unless he held onto Walter's memories. Douche he may be, but he's a man of his word. And then in an incredible show of respect, he steps back and declares Flynn to be the superior choice for the King of the new world.
Akira's resolve in both alternate Tokyos. Blasted Tokyo Akira is prepared to take on hordes of demons if it means helping pave the path to rebuilding a Tokyo ruined by Law. Infernal Tokyo Akira becomes the King of Tokyo...because he wants to end the Might Makes Right rule of Tokyo and bring both the strong and the weak to equality. While the idea behind the White showing you both Akiras is to get you to realize the Vicious Cycle that Law and Chaos perpetuate, you also learn that society needs a good balance of order and freedom, as Blasted Tokyo is the result of too much Law and Infernal Tokyo is the result of too much Chaos.
Curiously, there's another such event in the case you tell Infernal Tokyo Akira you have your doubts about his plan. For a moment, he falters, wondering whether his philosophy is even right, and then Jonathan tells him he considers his choice the best one, and that he knows that it's precisely the hope of ending the violence in Tokyo and bringing true equality that truly makes him a worthy king. Akira is briefly left sputtering at this show of absolute faith in him.
Throughout the game, it's stated that Flynn is a good master to his demons, with the National Defense Divinities comparing him favorably to Tayama, and nowhere is this more apparent than when a demon returns from being Lost. Not a single demon enjoyed being away from Flynn, from the lowliest Slime, to the strongest Tyrant, to the Fiends, to the Archangels, and even an avatar of YHVH Himself, and each will tell Flynn upon returning how glad they are to have found him again.