One theme worth exploring in this book might be the influence of H. G. Wells' novel War of the Worlds on this novel. It's interesting that the invaders cannot breathe earth's atmosphere but must confine themselves to domed cities and most move about in protective tripods. These details seem very reminiscent of Wells' book; it might be interesting to compare and contrast the two works to explore what other themes they share.
One of the largest themes is Freedom. Protagonist Will lives in a small village under the rule of the unseen Masters, alien overlords who came to Earth and gradually took control through hypnotism and war, moving 20th century civilization back to Medieval times. Each year, young people of age are Capped, and their free will is taken away; while they remain much the same person underneath, they have no ability to think critically about their situation. Will rebels against the institution and goes on the run to find his freedom; he refuses to be controlled by anyone, man or Master, and the four books in the series reflect that need for Man to be a free entity.