I thought it might be cool to have an option to give your character derped eyes. :P
Derpy Hooves is such a cool character, and I'd love to be able to put her beautiful eyes on one of my own characters.
Colored primary feathers might be something to consider too, right? How cool would it be to have a cream coat with pink primary feathers?
Maybe other options should be available, like markings on the hooves like Shining Armor.
Freckles, too, would be awesome!
I don't know if you'll add these in the future or not, but I hope you at least take my suggestions into consideration.
Derped eyes is something I would love, though I would understand not wanting to put it in, due to so many players wanting it, and how rare it is in the show (only Ditzy/Derpy/Muffins having it). And having it as a wearable item instead of just in character creation would be... a little offensive, like a pony wearing something as a parody of the condition rather than the character actually having a lazy eye.
I fully support adding things to character creation like hoof coloration and perhaps coat coloration, as long as it looks natural (and not like the old Pony Creator stuff). Freckles are something that definitely is along this vein, and is almost impossible to abuse.
Unfortunately, while common in fan art, colored primary feathers are not something that the show uses. If LoE completely overhauled their character creation system to include more realistic horse colorations, then more realistic BIRD colorations would be definitely a fun thing to have. As it is, though, I see it as something that would be hard to code while not having much basis in the fantasy world of MLP.
On the other hoof, while I would understand that new models would be required (not a small undertaking), making the character creator more complex like that would be a worthwhile endeavor.