A very subtle one: Twilight has not one, but three pictures (four if you want to count the pawprint one) of Spike hanging in the walls of her room. This is most visible in the released background art (only one of the pictures is clearly visible during Twilight's nightmare; the one by her bed). Twilight really loves Spike.
It likely hasn't been that long since the events of the last movie, but Twilight's dream, before turning into a nightmare, has the rest of the group... Helping her pack, and generally being friendly and supportive, after she overslept and is running late to camp. It's pretty cute.
The students at CHS accepting Twilight and being overall nice to her despite what she done as Midnight Sparkle. Like Sunset, they understand that it wasn't her fault and forgave her; it also shows that they did learn from Sunset Shimmer's experience.
Sunset telling Rarity to lay off mentioning the Friendship Games after she accidentally reminded Twilight of Midnight Sparkle.
Sunset's official statement from the official My Little Pony Facebook page, concerning this movie:
"My friend Twilight Sparkle was there for me, and now it’s my turn to be there for her." — Sunset Shimmer
Later, when Sunset (as the first person) notices Twilight is troubled by something, she is very quick to ask if something is wrong. When Twilight is blaming herself for her actions in the previous movie, Sunset assures her it wasn't Twilight's fault. It's just very nice to see Twilight has such a close and supportive friend in Sunset now.
Gloriosa and Timber's very warm reception of the class upon arrival; they do their best to make sure they're comfortable and do things they'll all enjoy for the week, even taking suggestions from them.
The mere concept of the camp gift: the idea is for the current campers to create something to leave behind, that will be of use for future generations. Examples of previous camp gifts? The gazebo, the totem pole, and a sundial (which was made by Celestia, Luna and their fellow campers back in the day), all of which are there, years after they were made. The idea, besides leaving something useful for others, is to strengthen their bonds as campmates (and class). It's a very nice tradition.
Sunset's song "Embrace The Magic", a possible Good Counterpart to the Friendship Games "Unleash The Magic".
In that song, she encourages each of the group sans the absent Twilight to accept their newfound gift and learn how to use it. Really shows how she's grown.
There are also small moments of them helping each other and others; Sunset consoling Fluttershy who seemed unsure of her powers, Rarity's using her new barrier powers to save Derpy from falling into the water, etc.
Flash and Sunset Shimmer, in spite of being exes, seem to have developed a good friendship in this movie. Although it seems that they still have feelings for each other, now that Flash has moved on from Princess Twilight
Sunset showing some tough love to Flash and giving him advice to give up on Princess Twilight and move on shows that she cares about her ex-boyfriend and maybe still has feelings for him.
Once again, Flash is comforted by fan-favorite Derpy after his failed attempt to restart his relationship with Sunset.
The novelization makes it even clearer that at least Flash is definitely still interested in Sunset:
"Now Flash was distracted — by how the sun picked up the gold highlights in Sunset Shimmer's hair."
For those who don't mind Timber Spruce, Human Twilight and Timber's interaction at the end where Timber basically asks Twilight out and ends with them almost kissing, only for Gloriosa to come between them and take her brother away.
Nobody holds a grudge against Gloriosa, after she's been returned to normal. In fact, they all help her save the camp by setting up a fundraiser!
While there wasn't anything romantic about it, it's still extremely heartwarming for Human Twilight to say Sunset was beautiful when she was Daydream Shimmer.
During the bus ride, we saw everyone is excited to go to Celestia and Luna's old camp. It's heartwarming in two ways; Celestia and Luna get to share a childhood memory of theirs, while the students seem genuinely excited to go camping even if it's for a class trip.
Filthy Rich, despite being more of a Smug Snake than his Pony counterpart, is still an Honest Corporate Executive, if you think about it: his goal (to turn Camp Everfree into a spa resort) is actually pretty reasonable, he even gives a pleading Gloriosa more time to pay what she owes him, and he simply walks away quietly (instead of being an outright Sore Loser) when enough money is raised in time after all.
Gloriosa mentioned that he was an alumni of the camp, so it's possible he didn't want to shut down the camp, but saw too good of a business opportunity to pass up.
In this movie, Sunset is generally just so happy; it's refreshing after 2 movies of her being down and blaming herself for everything that has happened, so it's nice to see her genuinely happy for more or less the entire film.
When the paper lanterns are about to be launched, Twilight looks down at the flame in hers with a heartmelting smile, as if forgetting about all her worries for a moment.
By the end of the movie, you can see that life is finally turning around for Human Twilight. She overcame her demons and gets a handle on controlling her magic, learns a few valuable lessons about friendship, joins the band, and gets a nice boyfriend to top it all off. You can really tell that Human Twilight is taking her first steps towards growing into a wonderful individual like Princess Twilight.
from Gaea Everfree, who seems willing to hurt them all. Doubles as awesome. Especially when you consider, this isn't the magical sun goddess we are used to, but an ordinary human principal facing a magical being beyond her comprehension.