I only focused on ORAS since tue Hoenn region is my personal favorite and I enjoy the Pokémon from there best. There is some of the cast not included that I think i have better fits outside the Hoenn Pokedex (Nina with an Ursaring for example). But i only did the bachelor/ettes plus a few extras.
CARTER
Claydol would be his partner Pokémon. The reason I wouldn’t give him a fossil Pokémon is because he doesn't seem the sort to have revived them. He would definitely be studying the fossils but bringing them back to life feels more like Daryl (and we all know the scientist would not help Carter there). Claydol is still supposed to be an ancient clay figure brought to life so it would fit with the archeologist.
CELIA / CECILIA
I absolutely loved Wally as a kid. It was heartwarming having a rival who is a sickly kid that just wants a friend and you help them catch their first Pokémon. I'd want the same for Celia. It would be really cute for her to have a Ralts and with how bright a personality she has, I think a Ralts would be comfortable with her as well.
CODY / GORDY
I knew I wanted him to have a steel type and Aggron seems the best fit. I always picture the original Cody design where he's a bulky guy (and even with the redesign he's taller than most others in the valley) and I like Aggron matching that. While Aggron typically shows far more aggression in most Dex entries, there is an entry where Aggron will beautifully restore their mountain area if it's ruined by a fire. I feel like that tenderness and care aligns with the gentle giant Cody.
DARYL
The environmental scientist would quite obviously have Castform. In a crossover world, I could see Daryl having helped create Castform at the weather Institute before leaving to the valley to continue other experiments. Pokedex entries say Castform changes with humidity and changes in the atmosphere so I think Daryl would be able to use one to prep his experiments before the weather turned completely.
FLORA
Medicham is the best fit for Flora in my opinion. Her dialogue warns you about someone hanging around but she isn't concerned for her safety or seeking out the problem. Flora also strikes me as the type who when she focuses nearly completely ignores everything else.
GUSTAFA
I did consider Ludicolo because of Mirror B always coming out dancing with him and a catchy battle song for them. I think Gustafa would be better paired with Volbeat though. I think Volbeat would be a good partner for Gustafa because he is the Pokémon equivalent of a firefly and our musician likes stargazing. Volbeat also likes living near clear ponds and with Gustafa playing at the Goddess Pond it seems to align.
Coincidentally, Volbeat is also the name of one of my favorite bands and can match with Fireflies by Owl City which is some fun musical overlap.
LUMINA
Romana would have the Skitty or Delcatty in my opinion. So, I think an Altaria would work for Lumina. It strikes a good balance between cute and elegant so I think it would match Lumina’s younger appearance and grow with her. Altaria also sings in a beautiful soprano and could accompany Lumina on the piano.
MARLIN / MATTHEW
With his focus on hybrid crops, I feel like an Oddish would be a great fit for Marlin. Addison prefers fertile, nutrient rich soil and grows glossier leaves the better the quality. Marlin would be the type to ensure Oddish and his crops had the best soil available to grow their best.
MUFFY / MOLLY
I think her partner Pokémon should be Feebas and hear me out before you think I did Muffy dirty. Feebas is often overlooked for being shabby but can live just about anywhere. While Muffy is far from shabby, she seems so focused on finding love that Muffy spends some of her time depressed and dejected when things don't work out. I think her having a Feebas to shower in love as she finds love and confidence herself is a better fit. Then Feebas can evolve with her to the most beautiful Pokémon.
NAMI
I like Poochyena for Nami. The little Pokémon that tries to be intimidating to hide its cowardice I think matches well with Nami's cold exterior and hesitation to share her feelings.
ROCK
Spinda I think is the best fit for Rock as a partner Pokémon. The Slakoth line is there but with Slaking being such a powerhouse despite slacking off, I don't think it's the best fit for Rock. He is very upfront that he won't be working at all not half the time. Spinda's friendly appearance and tottering steps that are odd seemed a better fit for the eccentric Rock.