I suppose it might be that the point of the machine is actually to move the Pokémon themselves from one Pokéball to the other – we know that Pokémon in the anime do seem to be tied to their own Pokéballs (take, for instance, Pokémon Food Fight, when Ash has to drag Snorlax over a mountain because his Pokéball is broken – for whatever reason, he can’t just, say, stick Snorlax in Pikachu’s Pokéball for a few hours).  When you give a Pokémon away, you normally give away the Pokéball with it, so you don’t need a special machine.  Of course, that just raises the question of why they’re so damned possessive about their Pokéballs that they aren’t willing to let them go when they make a trade.  Could be some sort of weird throwback to a period when Pokéballs were rare and valuable artisanal objects – before production was automated and standardised, they might have been covered with valuable decorations, or emblazoned with a noble trainer’s crest, so that traditionally trainers would want to keep their own Pokéballs even when trading their Pokémon away.  Basically the machine’s function is actually completely insignificant for the vast majority of people, but they use one because that’s how trades have always been done.

I’m going to go with “because then we wouldn’t be able to catch them.”  This sounds like a cop-out, but it has the advantage of probably being the real reason for it, and maybe it can work in-universe as well.  There will inevitably be Pokémon trainers who want to catch these things, and historically would have had the right to take any risks they wanted in order to do so.  Almost all Pokémon can be dangerous if you’re not smart in your interactions with them – Ash almost got killed by a bunch of f$#@ing Spearow on his first day, remember – so once you accept the notion of allowing young people to do this sort of thing in the first place, it becomes difficult to start drawing lines.  Also, training is the first and most important way that people in this world have of interacting with Pokémon, so deciding that trainers aren’t allowed to do so of their own free will probably seems like a really extreme reaction to them – like “holy $#!t, you’re saying that these things are so dangerous we can’t even let the monster-taming nut-jobs near them?  RUN AWAY!”

You know, I don’t think I’ve ever actually heard it quite that way around.  I feel like the games and anime, when they leave hints about that kind of thing, are more likely to suggest that humans are from ‘Earth’ and Pokémon are the interlopers.  Putting things this way around is, I suppose, one efficient way of explaining why there are humans in this world at all, but I actually don’t think it’s the only way, and I’m not sure I can think of any other questions that it simplifies, particularly.

I’ve never really given Elgyem and Beheeyem the attention they deserve, but my thinking on Clefairy has always been that there’s actually an interesting possible alternative that gets overlooked.  Clefairy are capable of space flight and they’re obsessed with extraterrestrial materials and celestial phenomena… exactly like some humans.  That could mean they’re from space, or it could mean that they’re from Earth and interested in extraterrestrial exploration, just like humans are.  Having said that, though, I think the explanation Game Freak and the anime’s writers are probably trying to point us to is more likely that life on Pokémon Earth resulted from some form of panspermia-type event – a ‘seeding’ by organisms capable of surviving in space (rather than, say, some kind of bizarre Noah’s Ark scenario), implying that there may be other planets where descendants of the same species continued to evolve independently.  In the real world, people who favour this hypothesis will point to bacteria and other resilient microorganisms that might lie dormant on asteroids for millions of years at a time, but in Pokémon we actually have complex organisms who can survive in space for extended periods – namely, Lunatone and Solrock.  If that happened, though, it happened so long ago that it really no longer makes sense to consider Pokémon ‘alien’ – we’re most likely talking hundreds of millions of years for something like Solrock to give rise to the myriad species that exist today.  Humans might be descended from those first Pokémon, or they might be descended from microorganisms that were there already – it’s sort of hard to say why it even matters.  All of this… hrmm… conveniently fits with some of my wild speculation about mineral-form Rock-types being the ancestral state of all Pokémon (damnit, I hate finding evidence that I might have been right about Pokémon evolving from rocks), but then on the other hand, if I’m right about Carbink, they might even have been around since the damn planet formed in the first place.

One of these days I really need to try drinking heavily before attempting to deal with $#!t like this.  It might make more sense that way.