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Characters drive plot, not vice versa
This is the show's biggest problem, and in a way the one from which all the others flow. The most maddening thing about the show is how inconsistent its characters are, seemingly changing motivation whenever the plot needed it. The Angela Petrelli we previously knew, for instance, probably wouldn't have thought it a good idea to make Sylar think he's her dead son Nathan, yet that's exactly what happened in the preposterous twist that ended season three.
Shows as fanciful as "Heroes" need to be grounded by characters that are consistently motivated by what's inside them, not just what's happening around them. Get that back and a lot of other problems may melt away.