Technology
The book describes how technology, especially that of a naval military, is very important to win a war. Thucydides argues that a modern empire (remember, modern meaning 400 BC) is impossible without a strong naval force with advanced technology. The trireme is described as one such ship that is very important for battle, and the Peloponnesian War could not have been fought as well without it. The idea of strong technology in the victors of war has remained evident in modern history, especially the two World Wars.
Empires
A theme of the book is the effect of empires on the beginnings of wars. Thucydides claims that the Peloponnesian War was the result of Athens growing powerful, and Sparta being afraid of that amount of power being used against them in the future. Empires are the controllers of war, and they can control the views of what the citizens think about war. When too strong, an empire is not as reliable, as it can do what is best for itself rather than its citizens. Sparta was very strong, but the intellectual knowledge of the Athenians won over the physical knowledge of the Spartans.
Bias
Thucydides' work is thought by many to be very biased, most likely this fact being intentional. In contrast with the work of Herodotus, Thucydides rarely mentions sources and leads the reader in a particular way. At many points in the history, it is also evident that sources were limited or less limited, like the narrative after 4.108ff. Many of the actions, thoughts, and feelings of the players of the Peloponnesian War are inferred, which is against our modern legal system. Thucydides likely felt that he wasn't doing anything wrong, but bias in a work of non-fiction can alter history - and we may never know how much it actually did.