the science made the least bit of sense and that Phlox's dialogue matched what we see on the planet.
I haven't watched the episode in a while. From what I remember it does fly in the face of what we know about evolution. But maybe not. We only have one data set (life on this planet) from which to judge how evolution works.. it's certainly not unlikely, particularly in the Star Trek universe, for two sentient humanoids to evolve separately on the same planet.
I'm going to watch it again, but even if the science was failed, what's more important are the issues and the characters. Most of Star Trek's science doesn't match reality, but the producers of Trek always try to encourage their writers to come up with how the plot affects "our characters."
The episode was subdued, quiet and reflective, and, whether they made the wrong judgment calls or not, the characters thought deeply about the decisions they wound up making. I would rather have a thousand episodes like this than "Profit and Lace" or even "Dark Territory."