There is a long list of things I would do differently. Let us begin.
- There is no Student 6 or School of Friendship. That whole arc I did not like at all. I found it a very boring thing and I found it to be a complete waste of time. The Student 6 were not interesting to me at all, and the idea of a School of Friendship was rather corny at best.
- The School of Friendship is replaced entirely by arcs focusing on background characters such as Diamond Tiara, Silver Spoon, Lyra, Moon Dancer, etc. Fully flesh these characters out with rich and interesting details. Don't toss them off and forget about them.
- Twilight becomes a Princess, but does not take the "Princess of Friendship" role. Still does the same role, but I never liked that name. I know it's a show about friendship, but I think that's just too much.
- Rainbow Dash being an egotistical jerk to her friends is actually something that is addressed in the show - and something that gets her into trouble. It's a plot-point there could have been more to deal with, "changing" her ways, so to speak.
- There is more about Spoiled Rich. Make a whole plot about how she is actually Diamond's stepmom who is trying her hardest to be loved, but her nature is a different story. Don't just make her a "bad pony" without any background information. Have whole arcs and episodes dedicated to understanding her POV on things and helping her fit in, and make friends.
- Diamond Tiara is not reformed in an instant, but over a gradual arc to add more substance to her reformation. Focus more on her and Silver Spoon, and have more episodes about finding out about their families and such.
- Pinkie Pie is toned down a bit. I used to really dislike her. I don't feel so strongly against her, but I feel like the show would benefit from toning her down a little bit.
- Have AJ's parents explained in an earlier episode and tell more about them. Would still be Pear Butter and Bright Mac, same episode over all, but leading up to it there would have been scenes such as Apple Bloom getting curious and finding photos of them, and then asking about who they were, initiating the whole arc.
- Starlight Glimmer remains a villain and a constant threat for longer, the whole reformation is actually just a ruse for her to get more involved in finding out ways to defeat the Mane 6. Starlight's backstory is not what it was in the show, but is instead, something that leads to a complex ideological scene. Starlight genuinely believes what she is preaching, and does it with all the good intentions - but is blind to the damage she does to others. Starlight thus does not become a school counselor, because she remains a villain for longer within the show.
- King Sombra has a longer backstory befitting of the Comics, and Radiant Hope is in the actual show. His squeaky voice in Season 9 doesn't happen, and he remains a fearsome villain upon his return. More on that in a bit.
- The whole arc of the Changelings reforming never happens. The Changelings remain a constant threat and issue for Equestria. Thorax never exists, and instead we have an arc about Twilight and the Mane 6 learning about the Changelings. They are the way they are because they will die if they don't drain love, and they are a separate species from Equestria, there are other hives beyond Chrysalis. Perhaps there could be something to where there is an "Enemy of my Enemy" situation where when Tirek arrives, Chrysalis actually teams up with the Mane 6 and the heroes to defeat him.
- Tirek is a more fearsome villain akin to the G1 villain. He is genuinely evil and corrupted, with his desires to please his father consuming him. Discord still betrays the Mane 6, but as a consequence, regaining their trust is a constant issue he struggles to deal with after Tirek is defeated.
- Discord's reform takes longer and ends up turning into an arc throughout a whole season where he proves himself, and then has to prove himself again. Fluttershy still loves him dearly and there is a few scenes where Discord interacts with the CMC, Diamond Tiara, Silver Spoon, and the school. I think that would be entertaining.
- More Luna and Celestia episodes. Perhaps have it be less comical and find out about their origins, their parents, etc.
- No pillars of friendship. Make them each independent unique characters not connected to the other. Still keep the Pony of Shadows and have him be a villain that returns in the final, where the real Grogar gets all the villains together to make a league of Evil, a "final battle for Equestria" kind of thing that is an actual war.
- Chrysalis, would reform as well as Sombra, but Tirek, the Storm King, and Starlight do not. Would also bring back some of the older G1 villains, such as Lavan and others.
- The Map Table remains a plot point as well as Twilight's castle. Have more episodes dedicated to travel and exploring the world of Equestria, and beyond. Learn more about the Griffons, Yaks, and Kirins.
- Speaking of the Kirins, I would really want to see them again and have more follow up episodes on them.
- More Equestrian pre-history episodes. I wanted to hear more about Starswirl and not have him turn out to be a grouchy old dude who becomes enamored with a friendship school.
- Completely scrap the finale in the show from existence. Twilight will not grow up to look like Celestia, she will remain her normal size and gain a wavy mane at the end of the show.