This review of Troy in the The New York Review of Books, A Little Iliad, does a good job of explaining what feels wrong about the flick:

What sets the climax of the Iliad in motion is the killing of Achilles' beloved companion, Patroclus, at the hands of Hector--another loss, but this time one that propels the sulky hero back into vengeful action. Fueled, no doubt, by a desire to expunge the vaguest hint of homoeroticism from the proceedings --by classical times, the debate wasn't so much whether Achilles and his beloved Patroclus were doing it, as rather, as in Plato's Symposium, who was doing just what to whom--Benioff makes Patroclus Achilles' 'cousin,' a bizarre choice that (particularly in an era when family ties have never counted for less) has increasingly hilarious results as the action progresses. Watching Troy, you'd think that there was no higher value for the Bronze Age Greeks than cousinage. 'He killed my cousin!' Achilles shrieks at Priam when the latter comes begging for his son's body at the end of the story. 'You've lost your cousin, now you've taken mine,' a mournful Briseis (in this version, Hector's cousin) tells Achilles. 'When does it end?' This film's notion that entire civilizations were destroyed because of excessive attachment to one's collateral relations is, surely, a first in world myth-making.

War is hell, but you got to fight for your cousins!  ¶ 12:57 PM