Isabelle may have lived in the present, but she was created in future, by Marked-Tom from the future, with the powerful abilities of PFTF. Isabelle also in the beginning was more like the Marked, having a lack of human emotions (or very little of it) and unnecessary killing anyone that annoyed her. Isabelle was most likely created to be exactly how the evil PFTF are behind that great wall, and that is why I'm guessing the Marked originally had so much confidence that Isabelle would destroy the the 4400. Isabelle only lived in the present because she happen to be born after her parents was sent back to the present.

I think you're right-Isabelle was probably exactly like a typical PFTF in the beginning. Humanity didn't evolve very well, did it?

When Isabelle first grew up she was scared and weary of herself just as much others were. She loved her mother and father as much as she could, and she was terrified of Ross, until he got through to her. Then she started thinking just like the Elite.

I have the idea that the PFTF are on a seige for the Walled City. Their ace was to take the 4400 and send them back making sure that the City was never there in the first place, and the Elite sent back Isabelle to hitch a ride and kill the 4400 and ruin PFTF's plan.

Or something along those lines.

They made it clear that the Elite had the same information that the PFTF had because they knew about Richard and Grandmother Lily's relationship. Or...the Elite had moles in the PFTF and they picked Tyler for that purpose. If abilites are genetic, then the telekenisis that ran in his blood and Isabelle's was totally on purpose. The Elite knew about the plan from the PFTF the whole time.

What if Lily wasn't Isabelle's real mother. Marked Tom only said that Richard was going to be a father. He said nothing about Lily being a mother. Lily was just a baby carrier.

What is your definition of "mother"?

I know Lily was Isabelle's mother but I am taking more about DNA. Lily produced her but may be it wasn't her eggs that were used. Maybe they were from someone from the future.

Interesting theory on Lily, but given their time constraints on getting Isabelle in there, I think it would've been simpler to just use Lily and Richard and no one else.

I agree with this, IMO Isabelle was not completely emotionless, at first she was very emotional, the death of Lily and discovery of her powers, these things obviously affected her in a huge way. As time went on she belived she had no choice but to accept her fate, I am talking mostly about S3 of course. I also agree with PromicinDealer, toward the end of the season her attitude resembled that of which we have learned to be the Marked.