Stats first: Well, I’ve always assumed that a ‘Jolly’ nature meant jolly by the standards of that species.  A ‘Quiet’ Ludicolo, for instance, is noticeably less outrageous and excitable than the average Ludicolo, but still much louder and crazier than, say, a Jolly Yamask (basically a Yamask who occasionally manages to display a certain black sense of humour about being trapped in a perpetual living hell on the wrong side of the great beyond).  You might actually be able to use this to perform a rudimentary psychological comparison of two closely related types of Pokémon – Nidoking and Nidoqueen, for instance, are physically very similar, so Nidoking’s higher offensive stats and lower defensive stats might indicate a universal predisposition towards personality traits like loneliness, rashness, hastiness, and so on (which, of course, would tie in nicely with my ‘theory’ of Pokémon gender – link for new readers).

And stones: The exact physiological mechanism is quite beyond me, I’m afraid, but I did make a suggestion in this post that attempts to explain why some Pokémon use stones to evolve.  The conjecture, in brief, is that the forms triggered by the stones used to be natural evolutions of the Pokémon that have them, but have become vestigial because they’re no longer suited to changing environmental conditions – maybe achieving those forms has become too energy-intensive to be practical, or the species has come to benefit more from small size and agility than from power or intelligence.  They still have all the genes that code for the evolved form itself, but they no longer possess the regulatory genes that actually trigger the evolution, which now requires some outside stimulus (again, I unfortunately have no idea what exactly this stimulus is or how the stones provide it).  I imagine the split evolution patterns of Snorunt and Kirlia indicate something similar: those species used to evolve differently depending on gender (so, millions of years ago, all masculine Kirlia became Gallade and all feminine Snorunt became Froslass, without the need for a Dawn Stone) but, for whatever reason, Gallade and Froslass became unnecessary to the survival of the species, so that male Gardevoir and female Glalie gradually replaced the alternate forms.  This is, incidentally, a much easier account to imagine if you accept my belief that Pokémon don’t have biologically differentiated sexes, since there’s no need to explain how on earth Gardevoir started to develop male reproductive organs – in theory, a ‘masculine’ Gardevoir could always have existed and would have been able to reproduce normally, but they would originally have been weird anomalies, whereas now they’re perfectly ordinary.

This question continues:

“And in that instance, both balls were equally successful. But here’s the rub, in that you can’t re-use a pokeball. So how would you know if the master ball were really as perfect as advertised, (i[.]e. it will catch any pokemon without fail) if in that instance it was just as effective as a pokeball? If you caught a rattata with a pokeball, then doesn’t that mean you might have used a master ball? My question is, how can we know the master ball is really effective?

Oh! And another question, springboarding off of the one about what the pokeball means to the world in this series.

What would a master ball mean to your theory that pokemon battle trainers to test worthiness? That despite its resolve to test the trainer, it can be captured no matter what kind of fight it puts up, if it gets the chance to do so?”

 My answer is as follows:

Well, in the instance of the Rattata, you can’t tell.  That’s why you wouldn’t test a Master Ball against something like a Rattata; you’d test it against something a Pokéball probably isn’t going to catch, like a Dragonair or a Rhydon.  Testing a Pokéball and a Master Ball against a pair of Rattata is a little like testing a Roman Candle and a tactical nuke by strapping bits of paper to each one and seeing what happens.  Either way, the paper is reduced to ashes, but you wouldn’t conclude based on this test that a Roman Candle is equivalent in firepower to a nuclear bomb.

I’m not sure that actually resolved your question, but you might be better off consulting a statistician for a more thorough answer.

Anyway, your other question.  Assuming I’m right about what battling and capturing a wild Pokémon actually means, a Master Ball is a terrible, terrible thing to use.  It basically destroys the idea of a partnership between a trainer and a Pokémon and relegates the Pokémon to the position of a passive subordinate.  This really isn’t entirely above board, and it lends an interesting perspective to the ways Master Balls turn up in some of the games: in Red and Blue, the Master Ball is the object of Team Rocket’s whole Silph Co. campaign; in Gold and Silver, Professor Elm remarks that they’re only given to trusted researchers; in Ruby and Sapphire, it’s in Archie/Maxie’s office in the Team Aqua/Magma lair; in Diamond and Pearl it’s given to you by Cyrus, of all people, and if that doesn’t send up red flags then I don’t know what does!  Oh, yeah, and in Black and White, Professor Juniper is like “hey, look what I got you!  Isn’t it shiny?” so whatevs.

What you haven’t asked me, and the point where my model currently falls down, is how other kinds of Pokéball like Ultra Balls, Lure Balls, Dusk Balls and so on fit into the scheme of things.  At present, I simply don’t know.  Clearly they influence the Pokémon somehow, but how they do it – and what the implications for the series’ internal morality might be – is beyond me.  For now.