Pokemon is actually a super futuristic sci-fi game, we just see it as a Mon game
This is based around the assumption that the trainer in Brock's gym is correct when he says that you are 10,000 light years from facing Brock. As you are most likely two squares away from Brock, it can be concluded that each square represents 5,000 light years. The player character must therefore be some kind of interstellar battleship/carrier ship, and the Pokemon are fighters. Analogies:
When you capture a Pokemon, you capture an independent fighter, and crew it with your own men, or somehow convert the current crew into serving you.
The reason Pokemon do not die in battles is because the wreckage from the destroyed fighter can be repaired at a licensed "drydock" facility, a Pokemon Center.
Pokemon only being able to remember 4 attacks is due to limits on the size of the fighter's arsenal - each fighter only has enough structural hardpoints to mount 4 guns or missile-pods at once.
Power Points (PP) = ammunition for that particular weapon
Struggle (the Emergency Weapon) = ramming enemy fighter
HMs = weapons built into the ship itself
TMs = weapons that are mounted on removable hardpoints Standard Status Effects explained!
Poison and Burn are actually types of long-burning plasma or swarms of nanomachines that eat through the fighter's armour. Sleep
means the fighter's crew have been stunned.
In Confusion, a group of saboteurs or mutineers try and take over the ship. When the Pokemon hurts itself in confusion, the mutineers have temporarily taken control of a weapons system and used it to damage the ship. Though Confuse is more likely a computer subversion attack compromising life support or triggering some sort of scuttling effect, since you don't use "ammunition" when self-damaging.
Paralysis means that the weapons and propulsion systems are damaged.
Frozen means that the weapons systems are completely disabled.
Bind and so on are communications interference, making recalling the ship impossible. Either that or damage to the mother-ship's launch bays. Possibly a tractor beam.
Potions and other items are automated repair drones deployed by the mother-ship.
Legendary Pokemon are experimental fighters that have been produced only for research purposes.
Evolution and leveling are having your engineering teams look at the ship and its combat data and perform upgrades.
Breeding is leaving a couple ships with Central R&D to check for cross-compatibility.
You are only allowed six fighters because that is the maximum space in your mothership's hangar, and extra captured ships are kept at the dry-dock for when you want replacements.
That could mean Mystery Dungeon puts You in control of a squadron of fighters then,
Storylines explained: Rescue team series
: The player character's carrier sent on a wormhole research mission accidentally entering it forcing the captain to abandon in a fighter, thus also heavily destabilizing the (rather large) area of space on the other side of the wormhole. Explorers series:
The player character's carrier was sent on an exploration mission to the opposite side of a wormhole. The carrier arrives in an area in massive chaos. The carrier was destroyed by hostile forces/space accident, leaving the captain as the only survivor in a fighter. The captain, being unwilling to leave this area of space in its chaotic condition, decides to join a native group trying to fix the problem.
Belly = Fuel for a fighter, apples being fuel pods,
Items found in dungeons = Salvage left behind from other fighters
Randomly changing dungeons=The area of space being changed over time
Monster houses = Pirate ambush, the salvage (suspicious amounts of items in a room) is dropped by them to lure unsuspecting squads
IQ and skills = performance rating and upgrades to a fighter