I am wondering if this idea has surfaced? I am thinking that the affection and crush Daniel is showing toward Charlotte is nothing more then the love a father shows for his daughter because Charlotte IS his daughter? My thinking is that with the time traveling element introduced in the show, is it possible in a future episode the people on the island travel to say the year 1977 or 1978 and Faraday meets someone on the island say in the Dharma Initiative (possible since it shows him in the cave in the first scene which means he ends up at least pretending to be apart of the group eventually, falls in love, pregnates the woman and the baby they have together is Charlotte. It would explain Charlotte being born on the island and Daniel being awkward around her. When he sees her nose bleeding it could mean - and this is taking a page out of the original BACK TO THE FUTURE - that she is endangering Daniel from meeting ! his wife, hence her possible creation. Hence why Daniel now is ultra careful not to tell her anything.
Theory by Jon
Theory by Jon