Charlie lost his earlier in the mini-series...I don't remember "Why" he did, but he did.
There was never a reason given as to why the cross between a taken and an alien/earth was any different from a cross between an ordinary earth person and alien/earth person.
They stated that Charlie was special because he was from a line of "Fighters". His grandfather, his father and even he fought the aliens. His father even went nuts doing so. That didn't happen to "All" of those who were "Taken".
I think it's safe to assume that Charlie was chosen to breed with Allie's mom because his line was a "Proven" fighting line. If he, his father, or his grandfather wouldn't have been "Fighters", he wouldn't have been chosen...
I think maybe the aliens put all those things in all those people's heads just so they could track and then find the "Proven Fighter". Proven through three generations. Three generations being chosen as proof for whatever reason.