My favorite? Probably Create-a-characters that still have noticeable personality traits, so, it's probably a tie between Robin from Fire Emblem: Awakening and the Boss from the Saints Row franchise. I love these guy/lady/ladyguys because, as opposed to other silent protags and CHARs, They feel written into the plot instead of written around it, you know, as they are actual characters instead of walking plot advancement. They also can be a variety of colors, genders, and sexualities, so Choo Cho all aboard the diversity train!
Second place is the adorable Neptune, from the Hyperdimension Neptunia franchise. That's a series that I really only play for the characters(So It'd be nice if characters didn't just up and disappear every game. I miss you GUST), as the combat, story etc. is adequate at best.