I do not believe for a second that the humans are "gone" from Earth; they're
merely out of sight. Olimar himself even mentions that he thinks there must people natives watching him. There's literally a running stove in the Kitchen and a working freezer. And fresh food, including a ham. That house
is not abandoned. The only question is: How contrived is the explanation for why we never see other people? Is it a full=on slap stick "
Oh, you just kept missing them?" Or, is there a legitimate reason?
Here's my guess:
If you pay attention to the NPC chatter, the flat our comment on the game mechanics. They point out time flows slower inside of caves, the point out how corpses mysteriously vanish and reappear overnight, they comment on how it doesn't make sense for certain items to be in caves. They even comment on the fact that the Glow Pikmin do not appear to actually be alive. Thus, my theory:
There you go. What ever the details are, who knows. But something to the effect of the premise of
The Langoliers. Timey-wimey stuff.