What are the differences between the gods of Gilgamesh and the ones in Homer's Iliad?
The divinities in the epic of Gilgamesh seem a bit more closely tied to the forces of nature than the divinities in Homer's Iliad. In this respect, the deities in the Gilgamesh epic seem more like the divinities in Homer's Odyssey, especially Poseidon, against whose aquatic power Odysseus must constantly struggle.
In the Epic of Gilgamesh, we also see a divinity (Aruru) creating a humanoid creature (Enkidu).
Aruru washed her hands, she pinched off some clay, and threw it into the wilderness. / In the wildness(?) she created valiant Enkidu, / born of Silence, endowed with strength by Ninurta. (Maureen Gallery Kovacs translation)
The gods of the Iliad do not ever engage in this sort of activity.
The female divinities of Homer's Iliad do not engage in seduction of humanoid males, as is the case with Ishtar's attempted seduction of Gilgamesh. Aphrodite is a seductive divinity, to be sure, but we do not see this in the Iliad. In the Iliad, we see one goddess (Hera) seducing another god (her husband Zeus). This sort of behavior is more like what we see in the Odyssey, where the goddess Calypso keeps Odysseus as her sex-slave.
Although some differences do exist between the divinities of Homer's Iliad and the Gilgamesh epic, I would say that these divinities share more similarities than differences.