Who knows... (Pixel maybe?)
I think Sue's letter comments on how the humans had to work under the Doctor, researching the island, after he obtained the Demon Crown. Sue managed to escape at some point as her letter says. According to Momorin, she worked by the Doctor's side, until the seeds were found and she was thrown off the edge... Itoh... Well we know he was turned into a Mimiga.
Booster and Momorin must have been helping the Doctor with the island's research under threat. Itoh was probably not useful to the Doctor's plans. We know he doesn't even want to face Momorin at first... Perhaps the Doctor thought it would be a good experiment, as we know he is obsessed with the Red Flower. With kidnapping Mimigas. With recreating the events of 10 years ago, where Frenzied Mimigas were controlled and loosed upon the earth. If he can turn people into Mimigas, then he can control people as well...
But, apparently it's hard to distinguish between Mimigas... As Misery didn't even recognize that Toroko wasn't Sue. So, changing them into Mimigas was a mistake, since it allowed Sue and Itoh to blend in with the other captured Mimigas, and escape. (Or so it seems.) I would imagine Sue was being held hostage to force Momorin and maybe Booster's cooperation. That might make sense, as to why Sue was being hunted. Not sure they were really looking for Itoh...
So, I imagine the reason only those two were changed... Was that he needed the other humans as researchers to help his plans. And to hold Sue hostage to force them to work. That even if they could escape, Sue would still be stuck without the Doctor ordering Misery to turn her back. I would imagine Itoh was the first to be changed. And after confirming it worked, Sue next.
Though it backfired with their escape as indistinguishable Mimigas. Not to mention they were still smart like humans, making them a liability. Without the Red Flowers in his possession, changing them into Mimigas was trouble.
Oh, and the Doctor seems to be a maniac that might try experiments on a whim!
That would be my theory lol.