The Aeneid's main themes are those of conflict but also of the contrast between one's desires and one's duties as represented by the ideas of furor and pietas or piety. The story reflects the Roman idea that one must accept ones fate as handed down by the gods and to act accordingly and carry out one's duties before seeking to fulfill one's personal desires.
Though the Iliad addresses at length the idea of fate, its themes have far more to do with heroism and what makes a true hero. As the battle for Troy rages, various men present different images of heroes or try to and the story examines which is the most correct or most successful. Hector and Achilles and Paris and so many others are examined through the story as they choose different responses to the different problems presented to them.
In both, the gods play an enormous role in the outcome of the various situations suggesting in both cases that one ought to accept the fate handed down by the gods but also demonstrating the selfish nature of the gods that mimics that of humans or at times appears to outstrip it.
In my mind, the two themes are relatively similar in that both bring up questions about heroism, duty and fate and how they determine different courses of action.