In the Explorers games, the player can receive Eggs as rewards for missions or randomly in Spinda's Juice Café. These Eggs can be hatched in Chansey's Day Care, and you can then have them join your team. But these Eggs are unborn Pokémon, often of a species unrelated to the clients giving them out. Where did they get these Eggs? And why are they accepted as payment in exchange for rescue/bounty hunting services?! And why did that strange Pokémon at the bar just give you one based on watching you drink?!
When the player apprehends an outlaw, if the reward is monetary, Magnezone calls it "the bounty on this outlaw's head." Does that mean that the outlaws are executed after capture?
That phrase can refer to someone captured alive.
As a member of Wigglytuff's guild, the player must give 90% of what they make to the Guildmaster, and while the game doesn't make it clear whether this money is mostly for the guild itself instead of simply to line the Guildmaster's pockets, one of the ten "rules" for the guild is basically "Don't run away, ever, or we will hunt you down." Extortion much?
Does the ending of Pokemon Mystery Dungeon 1 remind anyone of Suicide?
The hero used to be a human. Assuming this, he or she would have friends and family... in the end, he or she stays as a Pokémon, so what can the friends and family assume? Their child would be a missing person... or worse, dead.
Since the human CHOSE to have their memories erased, it may be implying that the human had a shitty life and didn't want to remember it.
This is not true of Mystery Dungeon Explorers of Time, Darkness and Sky. After Darkrai pushes you through the time vortex, you unwillingly lose all of your memories and transform into a Pokemon.
This brought up by your partner in Gates of Infinity while who wants you to stay with them realized that you have friends and family who you love and love you back and would rather have you stay with them then being forever separated from them.
When Team Skull is staying at the Guild before the big expedition, if you look at the seating arrangement in the mess hall when the guild members are eating, the player character and his/her partner have to sit next to Team Skull! While they probably wouldn't intentionally stir up trouble in front of Wigglytuff and Chatot at that point, it would probably make for very tense mealtimes for the partner character especially, who is seated right next to Skuntank. The partner character doesn't necessarily know that Team Skull is playing innocent in front of Wigglytuff, and is probably worried about what Skuntank might do, especially if it involves both of them eating next to each other (considering that the infamous Perfect Apples incident involved stolen food, the partner character might be worried about Skuntank snatching his/her food). This could possibly make the timid partner character even more of a potential woobie.
Gates to Infinity mentions that there were humans other than yourself brought to the Pokemon World, except they're long gone now. Let's think for a moment... Weren't there two other humans we know of that were turned into Pokemon destined to save the world?
Except Hydreigon was talking about the other humans he brought to try and fight the Bittercold. Never mind the games almost certainly take place in different worlds (Rescue team is implied to take place in Humanity's Wake due to laboratory ruins, while Explorers' human, as far as we know, was native and not from a different world at all, both of which are impossible in the Gates to Infinity world), but Hydreigon specifically mentions having brought the humans to the Pokémon world, when he had no presence in the previous games.
There's nothing saying that the three worlds aren't one. Remember, one of them had to deal with Time Travel, what with distant futures and whatnot. Not to mention that it's also very likely that all of the games happen on different continents of the planet. So, for all we know, Hydreigon might've actually brought some humans that didn't get sent home.
The idea that the Pokémon are more bitter than they are in the previous games might seem somewhat arbitrary, but think about it — Post Town doesn't have anything resembling a system of Rescue Teams or an Explorer's Guild, and there was no place for Pokémon to submit requests before your partner started building Paradise. If you got lost, misplaced an item in a dangerous area, or otherwise got in over your head, you couldn't count on veterans to bail you out. No wonder most Pokémon felt their efforts didn't matter in the end.
This may be crossing into YMMV territory, but in the theory that all three games take place in the same timeline, what exactly happened to Hydreigon in Explorers: Darkness/Time/Sky during the bad future? Being the Voice of Life, he must of frozen (or worse) considering if the world ends, he dies, so if the world freezes, he freezes too.
More sad than horrifying, but you know in Gates To Infinity where the lights were actually humans being sent back? It was bad itself, but considering Hydreigon mentions to you that people will lose their memories of you when you vanish (doesn't happen), think of all the friendships the other humans made that are now forgotten in time. Or worse, what about the possibility of their companions getting slain or brutalized by Munna's gang? Imagine waking up somewhere and wondering why some mons beat you senseless.
The biggest one is, where are all the humans? While it could be argued that they don't exist here, not only are they mentioned, but both artificial Pokémon and what looks like remains of human architecture can be found. Was human civilization destroyed?
How do Pokémon's names work? All Pokémon are named like their species. Red Rescue Team had three Mankeys who lived together named Mankey, Mankey, and Mankey. All the Pelipper in the post office are named Pelipper. How do they stop from mixing up their paychecks?
Come to think of it, how do they deliver mail addressed to "Mankey"?
I was never sure how Team Skull got their name until now. It's because they're all Poison types, and a skull and crossbones is a common symbol for something being poisonous. Also, that same marking is on Koffing's body, so it could have been named in honor of him as well.
Chapter 3 of the Explorer games is called "The Scream." Playing the game through the first time, the player assumes this refers to Azurill's scream, which you hear in your first vision. However, you learn later that your visions are called Dimensional Screams.
There's a good reason why the heroes had to fight Primal Dialga in the second game first: if they showed who the game's real villain is early on, then the game would be shorter.
And speaking of Primal Dialga, look at his name in the wake of Omega Ruby and Alpha Sapphire... where Groudon and Kyogre gained 'Primal Reversion' forms. It may be a coincidence, but Primal Dialga seems stronger than usual, and Primal Reversion made the two aforementoined Legendaries considerably more powerful than their standard selves.
Why does Chatot assume that Team Skull is friends with the player character and partner simply because they know each other, or at least assume they're on good terms? Because he's gotten used to Wigglytuff, who considers everyone he meets to be a friend.
One of the NPCs in Post Town is a Trubbish who is somewhat self-conscious about his stench, and mentions that the main character doesn't seem to mind the smell compared to most other Pokémon. Considering garbage as a whole seems non-existent in the Pokémon world, they would be far more used to the smell of garbage than any of the other Pokémon.
When Azurill is trapped in a nightmare, it's mentioned that they can't feed him anything in that state. It's only fitting that the stage that takes place in his nightmare doesn't have any food and your hunger bar drops more quickly - you're suffering the same hunger Azurill is.
Grovyle learning Dig is unusual, as it is a move that Grovyle could only learn by TM and not part of the line's level-up moveset. However, the move makes perfect sense story-wise, as he would have purposely learned a Ground type move like Dig in preparation for fighting Dialga, since none of his naturally-learned moves would be effective against Dialga, but a move like Dig would be (Dialga resists Grovyle's Grass type but is weak to Fighting and Ground).
It could also be due to the fact that he would need a quick escape after 'stealing' the Time Gears. Tunneling though the ground sounds like a pretty good escape route.