lot of people itt not understanding eastern values.
the idea of obtaining oblivion isn't as negatively seen as it is in western culture, but that's because it's often framed negatively as being "erased" while you'll see more positive connotations in eastern culture as someone being "released." the whole point of buddhism is to escape the cycle of reincarnation afterall.
the whole series has been heavily rooted in buddhist philosophy from the start, so the idea that the ending is "sad" is one interpretation but that's ignoring a lot of the tenants and cores of buddhism.
one of them is the idea of attachments, ie you're supposed to let them go in order to achieve nirvana. and that is basically what Adamant was: a robot free of attachments, made to set the remains of humanity to rest. however, when he found the first gem, he inadverdantly created a attachment to the world by recreating them in the image of humans. this in turn broke him since he was now bound by desire and to the world. and in being unable to let go of that attachment, he unintentionally unleashed suffering on the gems that he ended up shaping into psuedo humans and imposing their values on them. what happens is thousands of years of suffering, for gems, Lunarians, and Adamant (maybe not the jellyfish, they've got their own issues but i don't know where they fit in). i think Adamant doesn't regret his choices, but in the end he sought release in Nirvana, just like the humans who created him, because he was unable to move on anymore.
another thing about the ending is that it very subtly shows the contrast of how Phos is treated when the gems following human values versus the buddhist mindset of acceptance the minerals and rocks have. with the gems, Phos was always being held back because of their fragile state and was frustrated because they were prevented from doing anything by the gems trying to protect them. in contrast, we see nu!Phos jumping around, chipping themselves and growing smaller, but the rocks and minerals don't try to stop them or hold them back. they understand that nu!Phos is losing themselves gradually, bit by bit, but they simply accept it. remember how the gems would freak out each time Phos would crack? notably none of the new rock organisms have that reaction.
in that sense, i don't think this is a bad ending or that Phos got left behind. Phos finally recieves the freedom and belonging they had been craving in the beginning, while their humanity - the part of them that still remembered their friends after thousands of years of solitude - that had been left behind was able to reach Nirvana and be at rest.
anyways that's why i don't think this ending is anti-human. humanity had reached its end long ago; it was time for the universe to move on. if anything, i would say it's a celebration of how the human spirit can persevere and grow, with all the ugly bumps and warts. i won't deny there were parts of the manga that i was not happy with - looking at you, cairnogem and all of the earth gems - but the ending was beautiful.