The whole character arc of the Cyber Newtypes (or just Four) and Phantom Pains. It was really nice to see Four getting along well with Sting, Auel and Stella, and the Phantom Pains return the favor, where they became practically best buds in the middle of war, despite being on the antagonistic side. Of course, this can get subverted into Tear Jerker when Auel and Sting eventually and undoubtedly bit the dust, but at least it can be subverted with...
Successfully completing the steps to save Stella (which is one of the highlights of how Z is considered the redemption arc of SEED Destiny). When Shinn is ready to sock it to Neo Roanoke, who's been revealed to be Mwu la Flaga, for not keeping his promise, all of the sudden Stella just ran off and glomped Shinn, calming him down in process, turns out Kira didn't fully kill her. Still, Neo/Mwu stated that technically he DID break the promise of putting Stella into a battle again despite his promises before so readied himself to get punched. Shinn, after seeing Stella alive and well along with learning how ugly it was to fight with hatred throughout the whole series, decided not to do it, he's done with letting his emotions get the best of him and leading him astray.
If the player chooses the ZEUTH route in Stage 56, Rey Za Burrel and Talia Gladys will avoid their canon fates and will fight alongside ZEUTH. Even after Rey considers Shinn his enemy and ZAFT disposing of Shinn's personal belongings for betraying them in favor of ZEUTH, Rey still held onto Mayu's phone for Shinn. Even with their friendship and loyalty at stake, Rey still held onto the phone in hopes that he would meet Shinn again on better terms.
Speaking of 'saving someone'... well there's also the time when you can successfully save Aki. Learning that she became a human bomb instead of being unaware of it till the end, Aki resigned herself much like Hamamoto despite Kappei's grief. Suddenly, Po intervened and stated that under the orders of Diana Sorel, who could stand the Gaizok/Butcher's brutality no more, she's there to bring the countermeasure to the human bomb: A lunar bed that will suspend whoever sleeps in there in stasis, which would stop the human bomb time from ticking, giving the Moonrace enough time to develop a way to defuse the bomb. While the other victims probably couldn't be saved, at least they could save ONE victim, and that happens to be Kappei's dearest friend. Kappei finally exchanged sweet words that he's gonna bring her a present while she patiently waits until the time they could reunite without the bomb inside her: World peace. Tomino's tendency for the show was at least curbed a little.
Provided you play your cards right, Charles and Ray Beams show up in the final levels, having survived their climatic battle with the Gekkostate. And this time, they're here to help Renton save Eureka, choosing their parental love for him over their hatred for Eureka and the Gekkostate.
What's more, after Renton evolves the Nirvash into it's Spec 3 form, Charles and Ray express how proud they are of him.
2rd Super Robot Wars Z: Hakai-hen / Saisei-hen
Shinn and Kamille seeing eachother again since after the last game in a battlefield is pretty sweet. Shinn is happier then you would usually see him, and both their love interests have to tell them to calm down and get back to the fight.
In Saisei-hen, if you have enough Zero points, Banjo and Roger will prevent the tragic death of Shirley in the Code Geass story, arriving just in time to prevent Rolo from killing her.
Additionally, Roger will reveal to Lelouch that he knows he's Zero, and later, Lelouch will reveal this to Chirico. In combination with Shirley's survival and the support of his allies (Heero also knows) even with them knowing his identity, Lelouch is much happier in this version.
You'll be allowed to choose whether or not the Black Knights betray Lelouch/Zero when Schneizel reveals Zero's true identity. Having them stay with Lelouch results in the Zero Requiem never happening, meaning that the Britannian conflict or at least the conflict of Code Geass end with Schneizel's defeat at Mt. Fuji. One of the good things that comes out of this is Rolo's survival and the reveal that Euphemia survived because Schneizel saved her. Unfortunately, Jigoku-hen would reveal that this alternate route is non-canon.
Shinn and Kira relationship has gone even better and is explored in one of DLC stage. Both Shinn and Kira swear to watch each other back in place of Lunamaria and Athrun, It's very heartwarming considering what happened between them back then.
Char fulfilling his promise not to drop Axis, something he's already vowed to do all the way back in the first Z game. Even when Full Frontal does it anyway, Char prepared for it, uniting the entire world against Neo Zeon. Even pushing back Axis itself was heartwarming, as Z-Blue joins Amuro in pushing back the meteor, and everyone uses their special abilities and powers and simply their combined will to push back the meteor. All the while, their friends and family are silently cheering them on back home on earth!
During a save-game skit, Noriko and Nono get to play with the former's action figure collection, which is quite adorable.
Brerabecomes much kinder due to his Character Development, as the Z Saga uses both the TV Series and Movie versions of his characters, having him start of as a Jerkass as TV!Brera, but gradually develops him into a nicer person as Movie!Brera. As such, he acknowledges Alto as his friend and eventually takes back his "I don't entrust Ranka to you" statement.
The ending has several moments. Namely when the characters are in a limbo waiting to return to their worlds. Many characters make peace with each other, such as the Sphere Users, which include those previously dead. And even Advent makes peace with Hibiki before passing on. Also EVERY ONE of the series featured, including the originals, has a heart warming scene where they are in their own world.
For Rei to do that should make every EVA fan drop their jaw and then aww.