We know Sakaguchi wanted to keep every Final Fantasy as a standalone game. When this game first came out, no one expected sequels. So when the game ends on an ambiguous note, many had no idea what to think.
And the nature of this Final Fantasy was different from anything we’ve seen so far. One of the themes was about life after death, and a second one was about a planet’s ecosystem. Sakaguchi wanted to express, in a video game, what happens to life after death. He also wanted to make a statement about the harm we do to the planet while mining for resources. The conclusion, I think, wasn’t obvious but logical. Humans are the cause of the threat. This means that the planet responds by removing them.
But no one saw this ending because no one really likes it. No one likes to think we wasted all of that time to save a planet which eradicates us. No one wants to think about the analogy to our world…
But wasn’t this the message? All of Shinra’s exploitations, Hojo’s experiments, AVALANCHE’s destruction, SOLDIER’s ambitions and Sephiroth’s scheming were ultimately meaningless to the planet. They were to make life better but made it worst. Look at all the mess the humans were causing to each other. Now they all go back to the source, the Lifestream, the Promise Land the Cetra’s spoke of.
Thematically, this seems to make the most sense. And who knows, maybe the Final Fantasy VII remake will actually make it clear that this is the canon answer. And shouldn’t it have been obvious?