1. Having Twilight revert back to status quo as if nothing happened. They've given her wings and radically altered the character, so they better have the balls to progress the story somewhat. Giving her princesshood and then sending her back to live in Ponyville to write letters of friendship all over again with nothing coming out of it will be a complete waste and feel like the result of shitty writing.
2. No mention of EqG. This doesn't really need explaining. It was an "interesting" side project, but that's it. By extension that means no Shimmer either.
3. Main characters getting any romantic interests. While it would also be interesting to see this, given that it's a children's show, it wouldn't be handled well and would feel tacked on, much like Tank. Maybe it'd get a passing mention in some episodes, but having to write the personality for a whole new character that would be interacting with a main character in such a way quite literally seems like it's beyond the talent of the current team.
4. Keep all fandom references out. This doesn't mean I don't like little nods, such as seeing Derpy or Lyra and Bonbon together in the background. But when it becomes distracting, that's when the problem starts. Having a character use the word "bronies" would be a perfect example.
5. Stop ruining characters. Trixie had no reason to come back, Discord had no need to be reformed, and Spike being incompetent was completely out of character. Please don't screw up Chrysalis even more than she already has been.
6. Stop with the superfluous padding. Why did Spike need find the book in the little space hidden behind the other books? Or what was the point of that sequence in which Scootaloo fell asleep and narrowly avoided danger just to end up where she started? It's unnecessary to add those things and they stick out like a nail.
7. Make Fluttershy's training with Iron Will actually mean something. It was season two and yet she's still acting absolutely timid and afraid of her shadow. That's not using her for comedic value, it's just plain bad writing.
8. On the subject of bad writing, it'd be nice if Polsky didn't write anymore episodes. He's been around since season one and yet still hasn't managed to write an episode that's memorable for good reasons.
9. Dragging stories out. Enough with the CMC trying to get their cutie marks, it's lost its charm. Enough with Rainbow trying to get into the Wonderbolts and only managing to "impress" them. It's been going on since the beginning and it's time to move onto the next goal.
10. Stop introducing characters and ideas and then not developing them. Both Shining and Cadance have the personality of a cardboard cutout, we'll never know why Lightning was such a (poorly written) bitch, why Luna meddles in dreams in the first place, or just what bat ponies are or where they come from. For all the world building the show likes to do, it seems to leave a lot of holes.
11. As for the world building, stop introducing places that suck. Equestria has some really interesting places that would be exciting to see expanded upon, but they only seem to focus on the really boring ones, namely the Crystal Kingdom as of late. Bluntly put, that place is shit. It's design is boring and plain, the mythology surrounding it isn't interesting in the slightest, and for being such an important place in Equestria, it never gets mentioned in seasons one or two. Yes, and I know that's because of the toy, but casting it as the old kingdom would have made more sense than it being some important site that just did a magic trick to disappear.
12. Don't make any direct mention of humans. There's no need to in a show about colorful talking horses.
13. Perhaps most importantly, no more damn alicorns. The last thing anyone really needs is the main cast getting ruined for another quick buck.