Legendary Pokémon
Ah, Legendary Pokémon. They're shrouded in myth and rumor, featuring prominently in legends (I'll give you a moment to get over your surprise). Every professor dreams of studying one; every trainer, of capturing one; every battler, of fighting one. But the question remains, just what are they?
For the moment, let's rephrase that question, as "How do Pokémon get classified as a Legendary?" Well, there are a few criteria, and to some degree it's a rather subjective process.
First off, Legendaries are powerful. I know, I know, I keep repeating that all Pokémon are powerful, but for Legendaries it's doubly true. It's said they can manipulate the seasons, control the weather, reshape the face of the planet, grant wishes, have power over emotions, and rule space, time, and antimatter. It's even said one of them created the universe itself. If they only have one-hundredth of the power that the stories give to them, still they are potent almost beyond belief. They are not invincible, but to the best of our knowledge, no Legendary has ever lost to a non-Legendary in a one-on-one battle; it requires a team to defeat one. On the rare cases they have been defeated, they've always fled, never been captured. In some cases they dodged Poké Balls as they fled, but in other cases they were allowed to leave.
Why would a trainer allow a Legendary to escape? Two explanations have been given by those who defeated them. One reason is that they felt unsure about their ability to successfully control their quarry, and dreaded their wrath. The other reason is that they believed capturing the Legendary would cause some kind of imbalance in nature that could ravage the world.
And to get back on topic, a second requirement for earning the Legendary qualification is rarity. We're not sure how rare exactly they are, but there's never been more than one of a species recorded at a time. To say that this causes debate among Pokémon Professors is like describing the surface of the sun as a bit toasty. One faction believes that they are true legends, and that there really is only one immortal member of each species. Another faction takes the opposite stance, that they reproduce like other Pokémon and that we simply haven't been fortunate enough to see them in family groups or as juveniles. A third faction, taking the middle ground, believes that they reproduce but also that there is one extra-powerful member of each species, a paragon if you will, that exemplifies their legendary, undying nature.
Which do I believe? Well, seeing as how this debate is nowhere near settled, and there's not really much evidence for any side (not counting the strange case of Manaphy and Phione), I've decided that I shouldn't state my beliefs on this controversial topic in a book meant for general consumption (I now cheerily await for all three factions to call me a spineless coward). That said, I feel fairly safe in saying there are two Legendaries, Mewtwo and Arceus, who are almost certainly one-of-a-kind. If this is not the case, I may never be able to sleep properly again.
As I said before, Legendaries are the subject of many a tale and story, woven deeply into mythology as gods. Normally this would be easy to dismiss as the wild exaggerations of uneducated folk, but to be frank, when it comes to Pokémon of this stature we don't dare dismiss anything until we definitively prove it false.
For Further Reading: Gods In Your Pocket? by Professor Pit Icarus