1) Most of the characters I already had a general idea of how I wanted them to look. The original designs were a conglomeration of what a few of the original voice actors wanted since they started the production with me. However, over time and through the redesigns, I drew them how I think they would look best. For example, with Jun, I felt a lack of inspiration to draw any more outfits for him because I did not like the way I drew his body. Therefore, I redrew him to make him more proportionate and made him fit a kind of playboy persona. Personality wise, they were just created through writing. We started with a basic concept for each of their personalities, but writing has brought it out more than just planning and outlining.
2) In my opinion, I would say either the Twins' or Jun's route. In reality though, each of the routes have their own charm and will be interesting in their own way. Each of the characters are important to the story.
3) I enjoy writing each one because they all have personalities that allow for me to feel like I can just pick up the phone and call one. The characters feel real to me since I'm obviously writing them, but I want them to have realistic qualities rather than just something flat and shallow. I probably relate to Rei the most out of all the characters--but it doesn't mean that I don't favor all of them.