"What needs to happen in the S4 pilots:
In my humble opinion that is. There were so many threads that were tied up and not tied together again that the show staff simply must do a few things in the S4 2 parter pilots.
Explicitly explain Alicorns and their purpose in general.
What are they really? Are they just pretty princesses that are there to be pretty and motherly and friendly to all, or are they something more perhaps? We thought we had Alicorns all figured out up until A Canterlot Wedding, and now it's all completely shattered after Magical Mystery Cure, and we can't see any clear picture. This point needs to be explained, because it's not only essential to the story now, it's essential to Twilight as a character, and what we're supposed to expect from her in the future.
Change the general premise.
I personally think that a show about Slice of Life like this, should never really derail from it's status quo. There's no definite continuity between episodes, except a general timeline between seasons. However, they've gone down the rabbithole now, and might as well explore the entirety of it. There's no going back now. They need to set up a new premise that makes Princess Twilight a good and, most of all, belivable change.
Give the Elements of Harmony and their bearers a new purpose
So, if we are to interpret Magical Mystery Cure correctly, the Elements of Harmony and it's bearers ultimate purpose was to make Twilight take the final step to ascend to Alicornhood. This simply can't be. There needs to be something more. Rarity, Applejack, Pinkie Pie, Rainbow Dash and Fluttershy might still be friends with Twilight Sparkle, and they are still the bearers of the Elements of Harmony, but they no longer have anything going for them. Now that Twilight is a princess, her friends are now her subjects. If this is not to be a bad thing, they need to be given a new purpose.
If none of this happen, then eff the show."