The Alternate Milla doesn't have anyone taste or even appreciate her cooking (namely her sister) until Elle came to her life when Elle tasted her cooking; complimenting it's good. Despite her attitude being all rude and bossy, she's actually quite sweet, caring, and even bonds with Elle until Milla sacrifices herself late in the game, and asks Ludger to make soup for her.
Had Agria accepted Leia's help, she would have become Leia's best friend and help her out in one of the fractured dimension. It's good to know that there's some heartwarming moments between those two if this incident happen in the prime dimension.
Likewise, one of Rowen's sidequests involves a fractured dimension where Nachtigal, the Disc One Final Boss of the last game, became The Good King instead of an Evil Overlord due to his sister's memento. He and the Rowen of that world were on completely good terms (even mention Rowen has affection for her sister), and while he does end up fighting you, it's treated more like a friendly sparring match than the tragic life-or-death battle of the first game. Even hearing his voice in a more friendly tone, compared to the last game, is heartwarming. Rowen ends up glad the two at least (sort of) got to meet again under better circumstances.
In one of the skits, Gaius tells Muzet and Ludger that being a king is so tough that he only gets to sleep for 1/2 an hour whereas his assistants gets a few hours of sleep. Both were shocked and then ask if he's alright. Sure enough Gaius suddenly dozes off while Muzet advises Ludger to let him sleep. Awww...
There's also the growth in his relationship with Muzet. Previously, she was more a tool to him than anything else, but now they're clearly close friends, and possibly more. In one skit, Gaius even says that blue has become his favorite color because he now associates it with Muzet.
Or for that matter, Muzet's new perspective. She was once so dependent that she was willing to slaughter countless people and destroy a world just for the sake of having someone to follow. Now she's learned to think for herself and yearns to bond with the people around because she has come to sincerely hope for a world where spirits and humans can truly coexist.
Muzet: A few special humans have turned me into a believer.
Jude and Mila being an outright Official Couple this time. Their interations in Jude's sidequests in particular are incredibly sweet. It does make it a bit of a Tear Jerker that she can't stay in his world for long, though.
The option to hug Elle after Alternate Mila dies.
The skit "The King and Elle", where Gaius, of all people, succeeds in making Elle feel better after Alt Mila's death.
The second chapter of Gaius's character quest, where he encounters the fractured dimension versions of the Chimeriad in a world where he never became King, meaning they can be openly kind and friendly to him. Once that chapter is over, Gaius comes to the realization that even in his world, with their subordinate positions to consider, they'd been his friends the whole time.
The third chapter is pretty sweet too. Ludger, Muzet and Gaius take Kyle and Tanner's group on a field trip to the Sapstrath Deepwood. After Gaius and co. slip away to quietly deal with some troublesome monsters, Kyle's group presents Gaius with a present: a camera. Kyle and Tanner give Gaius the nickname of 'Big E' and consider Gaius to be part of their group. They take a group photo after, with Gaius in the middle. It's slight, but you can see Gaius' happy smile.
After the battle against Rideaux and Ivar, the latter is once again humiliated that he failed at his job. This then goes two ways:
If Milla was picked to fend off the enemies, Jude will convince Ivar that failing is a learning experience and the two seem to reach an understanding. Considering the relationship the two had in the first game, it's nice to see that the two are finally on good terms.
If Jude was picked to fend off the enemies, Milla will admit to Ivar that while he has failed many times, she remembers the loyalty he displayed when he was her handmaid, and thanks him for his service.
A wrong number resulted in Elize unknowingly becoming pen-pals to the chancellor of Elympios. They briefly stopped speaking after Marcia sent a group of Exodus members to be executed, but they talked it out when a fractured dimension brutally knocked Elize out of her naivety. Marcia assured Elize that while growing up requires acknowledging the harshness of the world, it does not require changing who she is, and that people like Elize have a vital function in preventing everyone else from Jumping Off the Slippery Slope.
Just about everyone's final character episodes, especially Alvin's, condidering how badly he has it until then.
One of the skits mention about the tune Julius used to hum to calmed down Ludger when he and Ludger were lost on a camping trip when they were kids and he hummed it the whole time to keep Ludger calm (even he complain that he lost his voice after being rescued).
To be frank, ANYTHING that involves the Hymn of Proof, the song itself and the backstory. It was composed by none other than the Genesis Sage Kresnik, who was really just a normal girl named Milla who wanted to meet Maxwell. Even after they had a falling out because she couldn't support Maxwell's idea to save only a worthy few, her impact on him was so profound that he created Milla Maxwell in her image.
The way different characters hum the Hymn of Proof is pretty endearing. Julius hums it in an easygoing manner, even before he meets his fate. Jude and Milla hum it like a triumphant duet for the previous Maxwell. Ludger gives it a more gentle tone to Elle before he vanishes, and Elle herself hums it as a cheery tune as an adult.
The truth about Dr. Howe, the man who developed the theory behind spirit artes. It all happened because he fell in love with the great spirit Celsius and wanted her to feel the same. Like Milla Kresnik before him and Jude Mathis after, this caused him to throw himself into creating a world where humans and spirits can coexist. Celsius describes him as just a lovesick fool, but she may have returned his feelings after all. Seeing Jude and Milla together renewed her hope that her and Howe's dream has a chance to work.
Overlapping with Tear Jerker, Ludger choosing to save Elle from disappearing by sacrificing himself in the True/Good Ending. Like what Elize and Rowen say, he could meet Elle again as his daughter, but he chose her because she's the one that he grew to love like family.