The mother is always the source/contributor to the problems of the bad guys, even in real life. Look at the profiles of serial killers, all had mother issues.
I think Mohinder was engineered to save his sister. His father probably manipulated his genes/dna in utero or through some other means. He was born a few months after his sister died. Hence, he was too late to save her.
Well, we know Sylar's bad. It's the other's we're not so clear about. Examples; Claire's dad? Good, bad or grey? Parkman? Good, bad or grey? Nathan? Good, bad or grey? Peter? Good, bad or light grey? Like I said before, this is what makes the show interesting. Good people can do bad...
What I like is the fact that the line between good and evil is thoroughly blurred. I think we still don't know who is good or bad. Much like real life where there isn't really truly white and black hats. Just a lot of gray hats, some lighter than others.
I always thought that Sylar's power was the fact he could integrate the others powers by eating their brains. I assumed that if anyone else ate their brains, it wouldn't do anything other than cause indigestion.
I thought it was great that HRG thought that the Hatian was mute and we knew otherwise. I was yelling at the TV, "he can talk, he can talk". My wife was like jeeze calm down, we know he can talk.
All along I thought that good/evil hero/villan had not been established. I still think we don't know. Claire's father could be one of the white hats for all we know.
Could it be that Claire's dad is part of a government program that put the gene that causes heroism into these people? Therefore he knew where to look for null'n'void and Eden. The ol government conspiracy theory.