...you know he was a character in the Iliad right, the foundational epic of Hellenic culture? He was the son of the goddess Venus and a Trojan prince; and fought for the side of the Trojans in the Trojan War. He made sense to use as the central figure in the Aeneid because, although no match for the great warriors of the Achaeans (Greeks), he is personally saved from death in battle by the gods on several occasions – as if he had some great destiny to fulfil. Well, what greater destiny could there be than the founding of Rome?

Attributing the founding of Rome to this Trojan prince Rome the direct descendant of an ancient and mighty civilisation with a heritage that rivalled that of Greece instead of something that just sprang up from obscure origins in southern Italy. It also gave someone like Julius Caesar who claimed direct descent from Aeneas divine lineage.

also, I don't think it is in fact two separate stories you're looking at, if I remember correctly Romulus and Remus founded Rome and are descended from Aeneas – Aeneas never lived to see Rome; his mission was to settle his people who survived the Trojan War in Italy so that they could one day found, in the words of Poe, "the grandeur that was Rome."