They need to do more with Twilight Sparkle.
She was given interesting traits in the first season, but none of them really seemed to play out.
- There's her name; Twilight Sparkle is a very interesting name with the context of the entire day/night history of Equestria and the relationship of the Royal Sisters, what with twilight existing at the interims between day and night. May have been played out with Twilight helping bring back Luna. But it would be cooler if they did more than that, like having Twilight help the sisters reconcile in season 2.
- She has a great deal more magical power and talent than most other Ponies, even before she gained the Element of Magic.
- There's her whole mane and tail bursting into flame in Feeling Pinkie Keen. It could have just been a visual metaphor (like when she drank the hot sauce in episode 1) for anger/frustration, but it'd much cooler if some sort of plot point was made out of it, particularly since it's implied that her doing that was supposed to be a major "doozy."
The other ponies also have unique traits that were only briefly touched on in season 1:
Rainbow Dash: Has a rainbow streak behind, unlike other ponies, and can accomplish a Sonic Rainboom. Touched on, but unexplained. At the least the concept should be explored more.
Fluttershy: The whole Stare thing...yeah, that deserves some development.
Pinkie Pie: I get she had a dreary childhood, but I don't think that explains a psychotic break into delusions and bi-polar moods.
Applejack and Rarity also have their quirks, but I don't think they're as extreme as the others.
Edit:
And just because.