There is another explanation. Bare in mind that this is only a theory, and it is a videogame, some creative liberty will be needed and there is no official explanation.
Beware minor spoilers for the PMD games
Answer 2 isn't impossible, and we cant really disapprove it. At the same time we can't prove it. There is however more interesting and plausible theories.
Answer 1 have already been proven true as Pokemon and humans exist together in the main games and your main character in the Mystery Dungeon games is a human. In the PMD Explorers games it is also proven that there are humans in the future. Furthermore, the Pokemon in the PMD does know about or have meet humans, albeit they don't seem to like them or they outright fear them. We could thus assume the PMD games take place in the same universe as the main games.
So why is there so few humans mentioned in the games, and why did the Decrepit Lab fall into disrepair? And why do the Pokemon fear humans?
My core theory is that the Mystery Dungeon games takes place a long time after the main series of Pokemon games, in a time where all humans have died out for some reason.
But what could be the reason for humans disappearing and Pokemon fearing them? My first theory to this is that humans destroyed themselves through some sort of war. We can also assume both conventional weapons and Pokemon was used in this war, thus making Pokemon fear them. However, in all previous wars in real history there have at least been some survivors. An all out nuclear war could have killed all humans of, but then there wouldn't have been any Pokemon left either. So how do we kill of near all humans but leave Pokemon alive?
This is where my second theory comes in. A war between Pokemon and humans. For some reason the two fought a war that exterminated the humans. For all the fancy weapons we have today Pokemon could easily use their natural strengths and numbers to turn us into minced meat. But all the power in the world means nothing if you cant organise your ranks. If Pokemon were to have a chance of winning such a war, they would need structure. And wouldn't you know, the PMD games prove this on so many levels.
In the all the other Pokemon games/manga/anime Pokemon are very animalistic. We see them communicate among themselves, but not a whole lot more. They are capable of independent thinking and seem smarter than your average dumb beast, but they still seem content with being put into small balls and fight each other. They are still animals, or at least not smart or willing to rebel against us.
In the PMD games however, Pokemon have developed and entire society. They can write, build houses, organise themselves, they have money and a economy, they sell food, gear and even land amongst themselves, they plant apples and have developed some sort of higher agriculture, they even cooperate to solve advanced problems together. Heck, they even have weapons and fancy gadgets of their own that can do a bunch of stuff in the form of the Orb, throwing and seed items. These items are also interesting for another reason. They aren't in the main games. These items are never mentioned in the core game, so could it be that they were developed by the Pokemon themselves?
We could assume the Pokemon either had to create this organisation to combat the humans, or that gaining these human skills allowed the Pokemon to rebel against their former masters, this is basically trying to determine if the Pidgey or the egg came first. The bottom line is that the Pokemon in the PMD games are far smarter than the Pokemon in the main series of games, and that this could be linked to the destruction of humanity.
Speaking of this advanced gear, isn't it strange that these devices of teleportation and sticks of pure silver just lie thrown about? Its unlikely that someone put them there intentionally, but being left behind, such as at the end of a war or because they weren't needed, would give good reason for these items to be about. They aren't natural items either, then they would be in the main games as well. Manufactured goods aren't just going be scattered around for no reason.
See the comments for my rant about wild Pokemon in the PMD (its important but not vital to the question and theory itself)
All this would explain the Pokemon's fear of humans, the Pokemon still remembering humans, the Decrepit Lab's ruin, the advanced society of the PMD games and the lack of humans in the PMD games. A Great Pokemon War would explain a lot about how the entire PMD games are built up, as well as making up a interesting lore behind the games.
As I said before this is all my personal theories, and there is no backing by any official sources of this. But in this case there might just be a bit more to it than the usual artistic freedom.
