Tom Bombadil could be left safely on the sidelines for the most part - within his (self-imposed) boundaries, he is the Master, but he does not concern himself with what lays beyond.
According to
The Encyclopedia of Arda Tolkien has stated definitively:
quote:
"There is no embodiment of the One, of God, who indeed remains remote, outside the World, and only directly accessible to the Valar or Rulers."
The Letters of J.R.R. Tolkien No 181, dated 1956
so Tom is not Eru, and in fact does not appear to belong to any known race or order of beings.
While attempting to recreate the great battles of the First Age of the sun would be fun, I''m not convinced an RTS is quite the right format for battles between forces capable of reshaping the earth, creating the sun, etc.
Possibly more profitable to explore the high legends with an adventure game or similar - tell the tale of Beren and Luthien for example, or some other of the great tales of individual heroics.