First there is the character design, invent something unique that makes the character recognizable and different from the others.
Then there is the pose (tricky but still important in portraits shots) : Is the character seen from slightly above (he's short) or slightly below (he's tall), standing straight like a I, or slumped, looking forward or away. This is part of character traits.
Specifically for pixel technique, take great care in the eyes: You should pixel them early, in order to align the face according to them. Look at the 3rd portrait in your FF V Advance protraits : The eyes are 4px wide each and define the entire geometry of the face.