My own assumptions/predictions on Hoenn human-Legendary pairs:
1. Roxanne - Regirock (Rock-type specialist paired up with Rock-type Legendary)
2. Flannery - Groudon (Despite not being a Fire-type, Groudon's schitck is that it sets up the sun ala Drought (or Desolate Land if Primal) and its Primal form is part-Fire-type)
3. Zinnia - Rayquaza (Her whole thing is being part of some clan worshipping this giant green sky slinky.)
5. May - Jirachi (mainly has something to do with her anime counterpart's little brother Max befriending the thing in a movie, plus you showcasing her in the teaser for Chapter 3)
6. Glacia - Regice (Same logic with Roxanne, but Ice-type)
Have no idea whatcha gonna do with the rest but good luck on programming this shit.
Viewing post in The Legendary Pokemon Breeder comments
You got Roxanne and Glacia right
Flannery and Groudon makes sense but I paired Groudon to someone else and Flannery was left with Registeel
Zinnia isn't in it at all, I'm MOSTLY basing my game more on the originals where possible and she only turned up in the remake
May and Jirachi aren't paired, but that's all I'm saying
Anyone who wants to guess, the other Human characters are Aqua Shelley, Magma Courtney, Liza (aged up of course), Pheobe and Winona
I made my own predictions before but I think I might be able to figure it out now
Roxanne - Regirock (confirmed already)
Glacia - Regice (confirmed already)
Flannery - Registeel (confirmed already)
Shelly - Kyogre (part of team aqua makes sense)
Courtney - Groudon (part of team magma makes sense)
Winona - Rayquaza (one of my original guesses makes sense to me because Rayquaza is part flying type and related to the sky so the flying type trainer would pair nicely)
Liza - Eon Duo (You confirmed they will be caught together and Liza and her brother are already sorta mirroring Latios and Latias so pairing the duo with Liza makes sense (also a guess I made originally))
Pheobe - Jirachi (process of elimination(I also had may as jirachi originally but funnily enough Pheobe Jirachi was my backup for if that was wrong))
May - Deoxys (process of elimination but my assumption for reasoning is that she wants the DNA pokemon because her father is Birch (assuming because it could also be Norman depending) and pokemon science and research and the like)
Also Janine is Celebi because of process of elimination and I read the comments so I know whats up.
im having a brain blast now im surprised about some of the pairings being wrong but im giving it a second shot now that i did a little more research
Winona - Deoxys (Winona being the sky obsessed person she is may have seen Deoxys meteor) (I am still surprised shes not Rayquaza, Rayquaza is on one of her teams in B2/W2 but I can't read minds or control you so write what you think works)
Liza - Jirachi (process of elimination, it hard to figure out Jirachi because there is no location to find them in game so frankly they could go to anyone) (curious what your plan is with that fact btw)
Pheobe - Rayquaza (She trained at mt pyre, where the red and blue orbs are located so she would know about the legends most likely and be curious to meet Rayquaza)
May - Eon Duo (I dug deeper because I dont have super deep pokemon knowledge and Norman who can be Mays dad gives you the Eon Ticket to go the southern island so I think thats the connection here)