One other bit of background - the animated episode "The Slaver Weapon" was an adaptation of one of Larry Niven's "Known Space" stories, and brought some elements of that setting into the Trek universe. In Niven's setting, several billion years ago the galaxy was dominated by the 'Slavers', a powerful race of telepaths who mentally enslaved all other lifeforms. Eventually, one of their slave races managed to rebel against them, and the Slavers, rather than face defeat, used their powers to make every sapient lifeform in the galaxy commit suicide.

In the Trek universe, this could explain why the ancient humanoids were apparently the only intelligent life in their era - they could have been the first race to evolve after the Slavers wiped out all life, or had been somehow protected from the telepathic attack.

The Slavers themselves were humanoid, in that they were bipeds with two arms, but other than that didn't look much like humans; certainly a lot less than the hundreds of species all but identical to humans in the modern Trek universe.