What Could Have Been: The obvious example is how volume 3 was cut short, with plot threads obvious to be related to the main story ending up going nowhere. A bigger example would be the entire style of the series: The original intent was to have a revolving cast, with most characters not returning in future seasons. What could have been, indeed, if after season 2 we didn't have to deal with most of the extended Petrelli family?
Also, the Aborted Arcs caused by the writer's strike, which led to the Seasonal Rot which the series never fully recovered from.