I think they could have stretched it out to another episode. It's like boom I'm Sylar and I'm here to save you and then ooh will I kill Doyle or not? Then it's like no, we don't believe Samuel can do that and then 5 mins later they all run away scared. And all of a sudden Peter flies into Samuel then takes his power and they do a tug of war until he is powerless. They could have expanded the fights and struggles and added even more suspense but the only problem I see is Sylar is too powerful so Doyle was no problem at all for him.
I think it'll just be the start of the "future" we have seen glimpses of. Something will happen with her and Peter and she'll become brunette and chase after specials while Peter will get his infamous scar. And if they write it well enough then I'm sure people will want at least another season. I think Hayden did a photoshoot with brunette hair. I don't know if it's really recent but if it was then maybe it points to her character in Heroes being brunette.