Taken as a pair, the films chart the decay and decline of the Greek gods, as they lose their power over humanity and disappear. At the end of Wrath of the Titans, there is only god left standing, perhaps reflecting the shift from polytheism to monotheism. All of a sudden, the Christian imagery made a bit more sense, as the gods here seem to depend on mortals to define them, even if the structures (life after death, etc.) appear to continue existing without human belief.
As the Greek belief system is wiped away, it's replaced with the trappings of Christianity. Zeus spends a portion of the movie with the flowing white hair and beard we associate with the Judeo-Christian God, for example, the film is structured are trinities and trios, and the new god, Hephaestus, is addressed in terms that seem borrowed from Christian theology like "the maker" and "the fallen one." Hell, even the minotaur roaming around Tartarus looks more and more like a Christian demon with a horned head.
Given that, in the real world, there's an argument that Jesus Christ's portrayal was influenced by Greek stories of demi-gods and the way that religions tend to coopt ideas and beliefs (and even gods) from other systems, perhaps Wrath of the Titans is about that happening in-universe. More detail on this theory here
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