Theme 1: proper politics, effective governing, and the correct way to use the military and fight a war. Machiavelli's big change from the norm at the time was to see the military as a natural extension of the political part of government. He purported using the military to help get political agendas accomplished. Not so much within the country's own borders, but to help with international relations. He figured that as long as the neighboring principalities posed a threat, why not look at them through a military point of view.
Theme 2: I will call it a free will theme. Machiavelli called it prowess vs. fortune. Modern day scientists would call it nature vs. nurture. Machiavelli spends a fair amount of time analyzing how and why a prince might be successful. Is it because of their own ability (prowess), or is it predetermined by their bloodline and circumstance (fortune)? In other words, is their success because of their experiences and personal decisions (nurture), or is solely because of their DNA (nature). Machiavelli doesn't side with either case completely. He believes that both pieces are integrally related. He believes that a person (prince) can have great free will control over their circumstances, but also believes that total control is just not possible.