Of course, being more loving with Peter could simply mean that she had given up saving the world actively by then, and it was already too late to built up something with Nathan.

That's my current favourite explanation, too - Angela during Nathan's early childhood being busy with world-saving and dealing with her returned from Vietnam alternating between depression and "I have a new mission" believing husband, but by the time Peter is a child having given up on it. Of course, there is yet another possibility, depending on whether or not Angela is a precog, and just how her ability shows itself. After all, the writers could have taken more than the Ozymandias plan from Watchmen. Dr. Manhattan in that comicbook finds it harder and harder to relate to aber people because to him, the timelines are so transparant - i.e. for example when he meets a girl for the first time, he also knows already what their first kiss will be like, when they'll have sex, what she sounds like when they break up.

never mind a slap! For telling her that he feels a connection!)

I remember some people during the hiatus speculating that she does that because she figures out his knowing about Nathan's accident means he manifested, and she doesn't want that, but the conversation she has with Charles sounds as if they expect Peter to manifest, so it's more likely the "Nathan and I are connected" part that caused the slap.

not to mention that telling one of your children "you are my favourite" is more dysfunctional than sweet. Of course, judging from Nathan's words in Six Months Ago, the Petrellis seemed to be pretty open about these kinds of things, anyway.

Quite. Daddy Petrelli probably did it, too. *marvels again that Nathan and Peter aren't even more dysfunctional* I think the age gap was what probably prevented the boys from doing the usual thing and becoming rivals as the result of that, which is what favoritism by a parent usually results in. Instead, you get the idea that if there is any rivalry, it's between Angela and Nathan about Peter, and might have been between Peter and Dad about Nathan.