I always had the impression that Lavos was the distinctor.
In the Reptite/Dragonian timeline, Lavos never fell, and thus the Reptites never died off and evolved into the modern-day Dragonians. Their evolutionary path allowed them to evolve as one with the planet and they were in perfect harmony with the planet and nature itself.
Meanwhile, in the normal timeline, Lavos descended and destroyed the Reptites. Humans evolved as the dominant species and were ultimately at odds with the planet, were parasitic in nature, utilized technology to manipulate and control the planet... which may have been because mankind was "corrupted" by Lavos, their evolution guided by Lavos' intervention.
For example, compare the Terra Tower, which is the Reptite dimension version of Chronopolis, or the Dragon God AI, which is the Reptite dimension version of the FATE AI. The Reptite version were more organic in nature and were - in the case of the Dragon God - a literal elemental construct, compared to the completely artificial FATE program.
In the end, I do agree that humans are parasites of the planet... but I don't think the planet has forsaken humanity. After all, the Entity directly guides Crono and company to stop Lavos and save the planet (and the future), and it's implied that this Entity is actually the planet itself.