Today, we see that the Roman gods were obvious copies of the Greek pantheon (e.g. Mars being Ares, Apollo being Hermes, Jupiter being Zeus) But was this distinction noticed by the ancient world?

I answered a similar question a few years ago here: https://www.reddit.com/r/AskHistorians/comments/4u6bdw/were_the_roman_gods_literally_transplanted_from/d5nelxu/

tl;dr, Roman and Greek gods are both derived from a common source, rather than the Romans copying the Greeks (although in their long history interacting they of course influenced one another).