Littlepip's eyes are either green or brown. its mostly up to the artist as she was never fully described. so they can be any color you like. but I do prefer Green eyes myself, though. they just look better on her.
Ha, I originally went grey. Anyway, I agree. Before this version of Littlepip solidified, I found some that looked a lot like Twilight. But I ended up with green out of preference for the general census.