Pewter City
Run by Petra, Brock's daughter.  See her profile for more stuff about her.

Cerulean City
Run by Misty's sisters, who are now a lot older and considerably smarter, too.  They're all married as well, and their husbands live with them in houses near the gym.  When Aoife gets there, she fights Daisy's daughter, Rose.  The Pokemon she has are Staryu, Seaking, Gyarados, and Horsea.

Azure City
This is a new city, and you know the path you take in the game to get to the Rock Tunnel?  It's around that area.  The gym leaders are twin sisters, Sora and Raven Starling.  Sora's profile is up and you can see it here.  They train flying Pokemon, and they have the Stratos Badge, which is shaped like those wings you get on the airlines.

Vermillion City
Lt. Surge got drafted again and went back to the army, so his gym is being run by a woman named Rei who is a total bitch, which is not good news for Aoife and co.  She has Raichu and Electabuzz.

Lavender Town
Yes, this place gets a gym.  It's run by three brothers: Aidan, Kieran, and Ewan Specter.  They train ghost Pokemon, of course.  Their father is a channeler, and their mother is (surprise!) Duplica.  They own the Phantom Badge, which is shaped like a silver crescent moon with a purple pearly thing peeking out from behind it sorta (see image).

Saffron City
Sabrina, it turns out, married that Russian guy that was in Abra and the Psychic Showdown (whom I gave the name of Vlad).  She had a daughter named Sonya, who Aoife fights.  Sonya has Kadabra, Snorlax, Butterfree, and Hypno.
And you know in the game, how there's the Fighting Dojo?  It's in this fanfic, and it has an actual badge (the Meteor Badge, which is shaped like a shooting star) even though it's not an official league gym.  The leader is Ferio Crawford, and you can see her profile here.

Celadon City
Erika's still there, but she's like 40 now (and still looks about 26 thanks to her Vileplume wrinkle cream ^^).  Gloom evolved, and she still has Weepinbell, and she has an Iveon.

Fuschia City
Koga's still there, although he's not doing much in the way of Pokemon training, so Aya took over and you can get the badge if you beat her.  She has Sneezing (see the new Pokemon page), Ekans, and Nidoqueen.

Chartreuse City
This is a new city!  It's on Seafoam Islands.  The leaders are Danae Dragyn and Ruari Dragyn, who train dragon Pokemon.  Aoife fights Ruari, who has Dragonair, Gyarados, Denryuu (a new one from Pokemon Gold and Silver), and Lapras.  Their badge is the Tempest Badge, which looks remotely like this.

Cinnabar Island
Blaine isn't there anymore, he's been hospitalized for some reason, so he's replaced by Cloud.  Cloud is the name I came up with for the guy in Wake Up Snorlax with the Pokeflute, that hippie guy.  He has his Snorlax, and Blaine's old Magmar and Arcanine.

Viridian City
Giovanni left Team Rocket, so the new boss is Cassidy (Butch is her second-in-command, and yes, Jessie and James are still there too but they are now actually competent). She and Butch use Raticate, Drowzee, and a new Onix, and J&J have Ekans, Koffing, Likitung, and Victreebel as usual.  The problem is, Aoife has to fight three Team Rockets at once: the Bosses Butch and Cassidy, J and J, and the other B and C, Bonnie and Clyde.