Through the fic, Team Rocket performs two major genetics projects. One of them is the sekritlike Tribo, the other is the world-changing Orthan. Orthan is an anagram (click here to see what of), and a clever one too. The project itself entailed years of research into Pok�mon genetics, and months upon months of preparation for only several hundred test subjects.
Orthan itself transforms almost any Pok�mon into, basically, human-shaped creatures who look like someone's dressing like a Pok�mon. What good is this? Well, I'll tell ya. It increases their strength and intelligence severalfold. Orthan Pok�mon are, well, faster-stronger-better than most normal Pok�mon.
Team Rocket didn't consider the psychological implications of such a horrendous transformation, however. It wasn't out of cruelty, it was out of a strange combination of detachment and lack of consideration for the Pok�mon. It would be unfair to say that the repercussions weren't unforseen, although they certainly didn't stop the Project from going forth. Many Orthan Pok�mon become depressed, a few suicidally so, and are viewed as freaks of nature. A lot of trainers who had their Pok�mon stolen and experimented on don't want to associate with their former Pok�mon. Other times, a lot of Orthan Pok�mon don't want to be with their former trainers again. Former wild Pok�mon feel out of place in the wild again. Very few Orthan Pok�mon can cope well with their changes and at the same time have former trainers who will support them (Alex accepting a mostly-faring-well Marril is an uncommon reaction).
That isn't to say that Orthan Pok�mon are universally despised. They aren't. In general, however, the change was so radical and yet only an annoyingly large small amount (seven hundred and something) were modified before a security breach shut down the project, so Orthan Pok�mon are not only considered freaks, but they're also very rare. The Pok�mon League, as the government on anything Pok�mon-related, has a tough time deciding what an Orthan Pok�mon's rights should be.
Other random things about Orthan Pok�mon include the fact that pok�balls don't work on them, that they can't evolve by any means, and that despite the fact that they were once Pok�mon, the average Orthan Pok�mon doesn't very much like fighting.
On the whole, Pok�mon SS doesn't delve very deeply into all of this, although glimpses it offers of the aftereffects on the world are common. Orthan Pok�mon aren't even that well-known, however, since there are less than a thousand between all of Kanto, Johto, Hoenn, Orre, and Idama (a nonsensical Japanese-sounding word that I made up for the country the Neo League is in). Most people have never seen an Orthan Pok�mon, let alone met and talked with one, as such since Alex and Tschel move about in the world most people assume Marril is simply a human who dresses like a Pok�mon.
It's an anagram of "anthro", short for the word "anthropomorphic", or human-shaped.