Well, here's a few answers for questions asked lately.
Rocket X: There are two ways of explaining that. One indeed would be evading the question by saying that the simple logical explanation is that it's fantasy and fantasy doesn't have to make sense - but that's not the answer you're looking for, probably.
Another one completely detaches the attunement of PokéMon with nature and certain elemental planes and try to go wild with biological fancies. Fire types can be explained on the Bombardier Beetle/Pernese Dragon/Reign of Fire principle - two chemicals that are stored in different areas of the body and ignite in combination with each other, or one gas that ignites in exposure to air - or, in various cases, you could claim that some PokéMon have their own specialized biological mechanisms: For instance, saying that Charmander tail-tips secrete a flammable fluid as part of its metabolic process, and an array of quills at the tip of the tail rubbing against each other create sparks that make the thing burn, and thus the fire is and indication of its metabolism, explaining why the oxygen flame effect (the fire turning bright blue and hotter) occurs when metabolism is boosted, or why their flames extinguish when they die.
Water type -attacks- can be explained by using the environment as well as intricate layers and pockets of hydraulic muscles which can compress water to massive pressure levels, which are then directed through the PokéMon's mouth or specialized nozzles (such as on Staryu/Starmie, or Blastoise's cannons) - but that only explains the pressure and the nature of some attacks. As for where the -WATER- comes from in itself, I'm just as wtf'd about this as you are - because surely, something cannot be created out of nothing, unless if they all have an internal philosopher's stone, and wouldn't that make then
red water PokéMon?
The true answer I believe is somewhere in between - Water-types must be connected to some kind of water elemental plane. Either that or their biology has officially broken my brain. ^^
Proximitus: The simple answer would be: Fanservice. Eevee was originally planned to have only three forms, but since everyone loved it SOOOOOOOOO much because it was so ZAWMG CUTE and the whole split evolution thing looked awesome... Game Freak just got crazy with the cheez-whiz and moments later we had like OVER NINE THOUSAAAAAAAAAND forms.
Now for a more logical answer: The Gen1 PokéDex explained it as having unstable DNA prone to spontaneous mutations. But as anyone with a bit of knowledge in biology can tell you, that's utter bollocks. Spontaneous mutations CAN cause a Pokémon to change in odd ways, but it can also cause it to grow random cancerous lumps, or be born, instead of a fuzzy cute creature, as a naked, vampyr-fanged beastie with a penchant for human flesh. Again that's Game Freak trying to sound cool and knowledgeable and failing, a-la the impossible temperatures of Flareon's internal combustion core, Vaporeon's molecular composition, Jolteon's accumulation of 'negative ions' and Deoxys' identity as a 'Space Virus'.
So, unstable DNA? nyet. Complex DNA? certainly. Many different possible evolutionary branches, that can be rather easily triggered? Obviously. My
article on PokéMon Evolution on the main site should explain my theory on how PokéMon DNA really works, at least on the evolutionary scale of things.
So that's it for the Eevee subject.
HM moves out of battles would be irrelevant in a real-life type PokéMon world - as the whole badge thing is quite simply a game mechanic designed to prevent players from sequence-breaking. Badges aren't magical items with zomg powers over PokéMon minds. They are human-wrought metal thingies devised to show an accomplishment in a tournament-league-whatever organized by humans. And I can pretty much gurantee that if you show a ravenous, angry Tyranitar about to trample you and eat your mangled corpse your eight shiny badges, it will probably wonder why is that insignificant insect waving a bunch of funny metal pictures before its eyes and maybe wonder if they'll taste good going down - for exactly a second before proceeding to kill you anyway.
"LAWL RESPECT ME! I HAVE EIGHT BADGES!"
"... Oh, bugger off." (crunch)
Anyway - game mechanic to prevent sequence breaking, so there wouldn't be much need to explain it further than that.
Nurse Joys and Officer Jennies are all mass-produced clones bred in tanks by a shadow government organization for the exact specific purpose, and they're told they're all related to make them not ask questions about why they all look the same.
Seriously - the anime explains them all as being distantly related - second cousins, cousins, mother's sister's cousin's nephew's former room-mates, y'know the ordeal.
The fact they all look the same is easily explainable: Do you honestly think anyone at the animé team has the time or energy to come up with unique individual secondary-support characters with a recurring role that ultimately mean nothing in the long run?
... Don't answer that, on second thought. Since that's about the role of every secondary character in the anime, other than to show off a new critter.
Thing is, they have the same role, so they don't need a new face. And it's a running gag. Like Team Rocket blasting off again. Other than that, your guess is as good as mine. (And I honestly like the idea of clones. >>)