I'm rewatching season 1 here and there and I was watching "Company Man" in which we see some Bennet flashbacks.
Remember Bennet shot Claude by order of the company? Do you remember why he was ordered to kill him?
Because Claude (the invisible guy) was 'harboring one of them' - he was raising a person who had special abilities.
Would it not make perfect sense if Claude is Elle's father?
Now, this doesn't mean for sure that that is who Elle called father. She might have been taken away from Claude by the company after Claude was shot. But I think that Elle's biological father is Claude.
Even more, this explains why the producers said that Elle had some stuff in common with claire. They were both raised by someone in the company after one of their parents (mother in Claire's case, father in Elle's case) was thought to have died.
Awesome? I think so!

