Hmmm... I want so many things, but... ^^ we'll see how much we'll get of these. I probably won't say anything that's not said before, since I'm definitely not that smart, but... we'll see XD
However:
Muuuuuch more Luna! <3 My hopes have gotten back in 3rd season when she started appearing more, but in first two seasons she was really underestimated. Maybe her back-story, maybe even her and Celestia's flashbacks about their childhood or simply earlier days. It would be nice seeing her coming to dreams again, or simply her everyday life. Maybe she should visit Ponyville again?
Rainbow Dash and Scootaloo. Enough said. I love them both, and I would really love to see their sisterly relationship they recently built. Maybe RD could help Scoots improve her flying abilities, or even be her personal coach in things she does to earn her cutie mark. They could have a episode just for themselves, so we could see more of their emotional parts (both tend to show no emotions, but not seem to be like that when alone). Simply, them hanging out =D .
More Zecora! Maybe even her flashback, so that we could see that "far away land" she claims to be coming from. More of her interaction with Apple Bloom (I always thought she had special connection with her). Blah, blah.
Crusaders getting their cutie marks. I know it sounds a bit story spoiling, but that would start a whole new era for them. Who knows what they might be doing after that? Scoots, Apple Bloom and Sweetie Belle don't appear to be the ones who'll forget about each other as far as they achieve their goal. Maybe they'll form a new club?
Seeing more of Alicorn Twilight life. That is probably going to happen, since she is a main character after all but still. Many details, like how she got accustomed to her wings, or crown, or how she goes with political life. Yeah, flying lessons from RD could be great, but not at the same time as Scootaloo, please =P . It would be also great to see how she gets along with her subjects, and, simply, how she feels as a ruler.
Sunset Shimmer and Flash Century. Not as boyfriend and girlfriend, though =P . I really got into them both in Equestria Girls, and I would love to see them back, as ponies - of course. Sunset Shimmer used to be Celestia's student, so it would be natural of her to come back to see her old teacher and apologize to her. I would personally love to see Sunset taking Celestia's place as a teacher at some point. As for Flash... well, I ship him and Twilight, so...
Less Rarity episodes. Sorry, but out of main character she had most episodes only for herself (maybe even more than Twi did), and that's enough. I like her, not to be mistaken, I only think she got too much credit already. Seeing more of episodes featuring her and Sweetie's relationship could be nice, though.
More Rainbow Dash episodes. She's the only one of mane 6 who still doesn't have a song for herself, which is a shame, since she's totally awesome. It would be nice to see more of her family, where she lives, blah, blah.
Scootaloo episode for herself. I'm tired of not knowing anything about that amazing CMC! Does that pony even have a home?
More cities. Really, all we've seen is Ponyville, Canterlot, Cloudstale, a bit of Appleloosa, and some more from flashbacks. I would love to see more of Manehatten (maybe Apples could visit Babs' family?) and all the other places they keep talking about.
A good villain. I can't deny it, all of MLP villains till now were pretty good, I just hope it will stay that way.
Seeing Discord as a good guy. He only appeared once in season 3, with no further explanation what had happened to him. Is he living with Princess Celestia and Luna in Canterlot, or is he living separately? What is his relationship with Fluttershy and rest of the mane 6? Is he still as mischievous as he used to be? There are sooo many things that need answers about him.
Twilight's early days in Canterlot. Yeah, I would love to see her thinking about how she started as a mare student, and now being a princess blah, blah. But anything from her old days in school. Being an egghead... I would love to see it =P
At least one more holiday episode, like the one about founding of Equestria! It's very interesting, and shows the power of friendship on a different level.
Basically, this, and many more stuff. If they used even 1/4 of all this, I'd be happy, but they probably won't. I can still dream though X) .