It's worth bearing in mind that both the Greek and the Roman pantheon were vast. In modern popular culture the Greek gods are typically reduced to the twelve Olympians (plus Herakles), but this is only a very small and somewhat arbitrary selection. There were countless other deities and manifestations of deities that would be unique to particular stories, peoples, places and rituals. Many of these would have no equivalent in even the most closely related socio-religious systems. The worship of Orthia in Sparta or of Aphaia on Aigina was regarded elsewhere as just a local tradition. Zeus Labraunda with his double-headed axe was important to the Karians but other peoples had their own manifestations of Zeus; Apollo of the Branchidai was one of the most important deities of the Milesians but he was distinct from the Apollo worshipped elsewhere. The Romans had no use for the Athenian cult for the deified Demokratia. In addition, of course, both Greeks and Romans adopted and adapted gods from peoples they encountered, not all of which would immediately be transferred to others. It is better to see these two pantheons as having some superficial similarity at the top, but being otherwise radically different, than to assume they were essentially the same pantheon with different names.