Tons of people are almost always going to compare Mass Effect 3's ending with the endings to another sci-fi game franchise, Deus Ex. After all, they each have an ending that destroys all technology so that they wouldn't be abused, another ending where the main-hero turns into a machine-god to control all technology, and a third where organics merge with their technology to create a new hybrid form of life.

However, I'd thought I'd compare MLP Season Three's ending with ME3's ending, which includes the following:

1. The Celebration of Friendship: As anyone can tell, Magical Mystery Cure's first and second acts were a homage to why we love MLP in the first place. Twilight had to restore her friends' cutie-marks to normal through the power of friendship, namely that each mare makes the other restore their own cutie-marks. We then have a musical number explaining the girls' personalities as they are restored, as well as their undying friendship with each other. Likewise, BioWare eventually released the final ME3 DLC piece, Mass Effect 3: Citadel, around the same time-frame as the premiere of Magical Mystery Cure. Like the first and second acts of MMC, the Citadel DLC was also a love letter to Commander Shepard and his/her strong bond of friendship with his/her crew of the Normandy, as they chase down a Shepard clone as a team and throw a party at Anderson's apartment, further solidifying their friendship.
   
2. Finishing an Unfinished Project: In Magical Mystery Cure, Twilight was assigned by Princess Celestia to finish Starswirl the Bearded's unfinished spell, which caused the cutie-mark switch-up in the first place. By the time she restores her friends' cutie-marks through the magic of friendship, she'd then rely on the combined power of her friends to finish Starswirl's unfinished spell. And guess what else was built during ancient times and left almost unfinished? Why, the Crucible from Mass Effect 3! The difference, though, is that while Starswirl's spell's function remains a mystery, the Crucible's functions would only be explained at the end.
   
3. Meeting with a God: Both Twilight and Commander Shepard were transported into mysterious places and met up with gods, including Princess Celestia in Twilight's case, and the Catalyst in Shepard's case. What both Celestia and the Catalyst were trying to do was groom Twilight and the galaxy, respectively, for the pinnacle of their evolution. And, their methods are morally questionable as well, from Celestia sending Twilight to certain death just to protect Equestria and build her up into a princess, to the Catalyst ensuring that organics and machines do not destroy each other by turning both sides into Reapers.
   
4. The Pinnacle of Evolution: It's at that point that Twilight grows a pair of wings and attains the title of leader of Equestria, while Commander Shepard has to decide between controlling the Reapers as the new Catalyst, destroying the Reapers plus EDI and the geth in the process, or combining synthetic and organic life. The difference is that Twilight was only given one choice, while Shepard three, two of which evolves either himself/herself or the whole galaxy, respectively. Plus, even with the Extended Cut endings, people still hate the Synthesis ending just because it homogenizes all life, just as people hated Princess Twilight for turning her into a god who would end up dominating her friends like an oppressive dictator.
   
5. Extended Cuts: Originally, both Mass Effect 3 and Magical Mystery Cure had vague, convoluted endings that left us confused and infuriated. But then story-expanding content was released to us to answer our questions, including the Extended Cut, and the book Twilight Sparkle and the Crystal Heart Spell. The Extended Cut revealed all the results of our choices in the entire Mass Effect trilogy, while ensuring that they are as different from each other as possible. Meanwhile, CHS establishes that Twilight chose to live with her friends in Ponyville, rather than move back to Canterlot just because she's now a princess. She also still panics over things beyond her comprehension, such as her wings and title, and is still dependent on a combination of her books and her friends to ensure her own growth and development as a leader.
   
6. It's Not Over Yet...: Right now, Season Four is in the works and will be released this November, and to tide us over, we had to watch a complete retelling of the first three seasons, but through a modern-day human teenager's perspective, in Equestria Girls. Meanwhile, there will still be a Mass Effect 4, it's just that it won't feature Shepard anymore.
   

So yeah, I've compared an M-rated sci-fi space-opera with a show based on toys for little girls, even though with the exception of what I listed above, neither of those franchises have almost anything in common other than a strong emphasis on unity and friendship.