This section applies to the ILCOE.
Alan's Pokémon are Pamela the Persian, Charlie the Charmander/Charmeleon/Charizard, Mist the Vaporeon, Racko the Grovyle, Victoria (Vicky) the Misdreavus and Diamond the Rapidash.
Pamela was bought as a pet for Alan when she was a Meowth and only later, after his first Ouen journey, became a part of his battling team. Her pet upbringing probably had a part in creating her vain personality.
Charlie is the son of Ash Ketchum's Charizard, brother of Mark's Charizard, and was given to Alan as a starter on his first Pokémon journey in Ouen. One day, he fainted in battle and regained consciousness in a Pokémon Center with no one around, where he evolved, too weak to resist it even though he hadn't wanted to evolve. After becoming a Charmeleon, he became quiet and moody and let Alan keep him in his Pokéball for extended periods of time, not liking to live with his forced Charmeleon body. Eventually, when Molzapart appeared to tell Alan to release Rainteicune, he used his Devolution Beam attack to try to restore Charlie's Charmander form, but thanks to a complication, this left Charlie in an unstable evolutionary state that caused him to change at random moments. After some time, Charlie began to gain control of this, however, and can now evolve and devolve at will. Though at first he tried to stay in his Charmander form, he eventually came to appreciate his Charmeleon and Charizard forms as well.
Mist was abandoned with a litter of other Eevee in a cardboard box in the city of Itsruban. Her siblings wandered off one by one, leaving her scared and alone by the time Alan found her and took her in, eventually evolving her into a Vaporeon as she had always wished to be. She chose to stay with him when he retired from being a trainer out of gratitude.
Racko is the son of Ash's Sceptile and was Alan's new starter when he set off on his second journey, in Hoenn. He loves the tropical climate of his native region and prefers it by far over Ouen's, but he chose to stay with Alan anyway after their Hoenn journey out of loyalty.
Vicky the Misdreavus lived in New Mauville, Hoenn, until Alan came along and caught her during his Hoenn journey. She enjoys his company and therefore decided to stay after he retired from being a trainer.
Diamond the Rapidash was caught after Alan's failed Ouen journey, primarily to be ridden, but she does not mind battling.
Alan's Pokémon aren't a very rambleworthy bunch, really; they're all very minor characters and more or less (besides Charlie) have just a couple of lines each if any, all of them in chapter 27. But I suppose some out-world rambling can be done anyway.
Charlie and Pamela are, of course, straight out of Molzapart and Rainteicune, and their nicknames reflect that, in the sense that they're obviously made as lame alliterations with their species names. Thankfully I never made up the rest of Alan's team at that time, since after all there he was just prancing around with Rainteicune for most of it. The other four were made up for their first appearance in chapter 21 of the original, where I had blessingly grown out of alliterative names.
Mist was actually a tie-in with a story I wrote sometime before the UMR, called The Second Clone, which included an Espeon called Mystic as a main character. In the fourth chapter of that story, the main characters traveled through the city of Itsruban, where they met Mystic's brother Shadow. At the end of the chapter, they explained that there had been five of them abandoned in a cardboard box, and they had all wanted to evolve into different evolutions and had chosen their names accordingly - Mystic, Shadow, Mist, Pyro and Wave. Alan was therefore supposed to have found Mist, the one who wanted to become a Vaporeon, and granted her wish.
Otherwise, those four were actually chosen to represent some Pokémon I really liked that Mark and May didn't have: Grovyle, Misdreavus and Rapidash, with Mist there mostly because otherwise Alan wouldn't have a Water-type at all and Vaporeon was my favorite Water-type after Gyarados and Lapras.