Necron is, as I see it, not as much of a "random dude that wants to destroy everything" as he is a metaphor for the destruction (or deterioration) of memories. If you think back, a whole lot of the plot revolved around lost memories (Zidane's past, Garnet's original home, Vivi's "origin").
Overall, I think the plot is not quite as loosely held together as it may seem at first sight. I'm not talking about Future Esthar style theories, I mean there is likely to be at least some thought behind it, even if you have to look for it at times.