In the manga, I believe Giovanni had some "Book of Secrets" which kinda showed that Giovanni was the first to know that Rhydon could evolve. I don't know... the boss of Team Rocket having not a Rhydon but a Rhyhorn as his ultimate made me wonder what they were thinking when they made FRLG. He may also boot his first Rhyhorn for a Honchkrow that he has in HGSS and keep his Kangaskhan in-tact... so in the end he'll have a Kangaskhan, Honchkrow, Dugtrio, Nidoking, Nidoqueen and Rhydon/(perior?).
Yeah, I believe we can have some theme for each people. Like... Phoebe can get a Dusknoir... keep her Banette and Sableye and probably get something like a Spiritomb... maybe keep one of her original Dusclops in-tact or evolve it into a Dusknoir as well? Or perhaps the other forgotten Hoenn Ghost: Shedinja. Just a thought. Planned out so far: (Dusclops/Dusknoir/Mismagius/Shedinja)/Banette/Sableye/Spiritomb/Dusknoir
Glacia can have one of her Glalie be a Froslass, keep one of her other Glalie in-tact and maybe stick an Abomasnow someplace to give infinite hail. Her signature is still Walrein, but what to do with her two Sealeos... no idea. Probably something with the elegant theme like Jynx and... something not Lorelei/Candice/Pryce-esque. Pretty hard to think about... but not Glaceon or Lapras or Mamoswine... all I can think of is a duplicate Walrein or possibly Cloyster or Weavile and MAYBE Dewgong. Contemplating. So it'll look like (so far): Glalie/Abomasnow/Froslass/Jynx/(Walrein/Weavile/Cloyster)/Walrein
Funny thing: those gym leaders with their second rosters always seem to get Pokemon from other no region out of nowhere... so it's hard not to have rosters that look ridiculously similar, but you can change their overall strategies. Like Morty and Fantina... Morty had two Gengars and a Mismagius that Perishtrapped instead of Fantina's Mismagius which was a straight out sweeper one.