Lovely topic!
I honestly for the love of me can't figure out who my favourite character from Biophilia is. The way I made (most of) them, they have qualities that are both good and bad, but they're generally self-aware and know what aspects of themselves they need to work on. Of the people that have had significant screentime so far, I'd say Helena is my favourite. She comes from a different background than most of her fellow students, but is very eager to learn and ask questions. She always puts in all of her effort into things and tries her best, and is respectful of other people and ideas. While she may seem ditzy and aloof sometimes, she's actually pretty plugged into the world around her and thinks a lot about things. One of the best things about her is how she can communicate even highly complex points with straightforward, to-the-point language.
In Bright Light, I also have plenty of characters that I love, but most of them haven't appeared yet. :3c But of the two main characters, Thomas is my favourite. Simply because I identify with him far more than with Ben. Thomas has a lot of things weighing him down and preventing him from fully realising his potential. But he works hard to overcome his fears and take steps towards the future he wants for himself, however small they may be. That he's helpful, kind and polite is only icing on the cake.