Oh yeah I knew about Illima making a change for Komala. Still uses a non-Alola mon at some point tho kinda like Caitlin uses Metagross sometimes. I guess Faba would be a better example from Gen 7 with his ace being Hypno
Some other examples I can find:
Eusine: Electrode (infact he doesn't have a Gen II Pokemon, his other known Pokemon being Drowzee and Haunter). Oddly you only battle him once, feels like you'd battle at least one more time with a more fully evolved team.
Brandon: While Brandon is mostly known for his use of the Regi Trio (think he'll appear in the Crown Tundra expansion?), that's only for the Silver Symbol, his Gold Symbol team is the Legendary Birds. Not sure if that counts or not.
Greta: Umbreon.
Anabel: Snorlax.
Dahlia: Doesn't have a Pokemon she uses twice. While she has a Dusknoir and Togekiss, she also has a Medicham, Ludicolo, Zapdos, and Blaziken.
Cheryl: Chansey/Blissey
Buck: Claydol
Mira: Kadabra/Alakazam
Marley: Arcanine
Battle Chatelaines: Not sure if this counts as they don't use the same Pokemon between their first and last battle. Nita and Evelyn are particularly notable as they never use a single Gen VI Pokemon. Also all their last battles are past Gen Legendaries (the grouped ones).
Sina: Glaceon
Dexio: Espeon
Mina: While probably not intentional, Mina has had Jigglypuff/Wigglytuff on most of her teams.
Lillie: Clefairy has been pushed for her for some reason.
Morty and Chuck get ragged on because they're some of the most glaring symptoms of Gen 2's bizarre phobia of using its own Pokemon that no other game aside from DP can match (not a single trainer in Morty's gym in either GSC or HGSS uses Misdreavus, for instance). As for the other two examples their problems do not stem from their signature Pokemon choice, hell I'd argue that if they just used a Hoenn/Kalos Pokemon respectively they'd be even more boring, at least with their current arrangement they have some novelty value.
While Chuck had a few other options (Heracross I think would have been fine), I can sort of forgive Morty as Misdreavus really isn't "ace" Pokemon material, though he could have at least replaced one of his Haunter with a Misdreavus.
I’ve been playing X again, and while the gym leaders are infamously forgettable, the gym designs are some of the best in the series. Anistar is my favourite, and I’m not so fond of Lumiose or Laverre, but every one of them has something interesting going on.
I feel the best Gen VI Gyms were Cyllage, Coumarine, and Anistar as they best used & showed off what the 3DS were able to let GF do.
Santalune & Shalour were just rooms. Santalune was platforms over a pit you travel via a spiderweb (could probably create a similar room on one of the DS games) & Shalour was just a roller rink.
Lumiose was the Hearthome Gym from DP.
Laverre was a vertical version of Saffron Gym.
Snowbelle at first looks like it effectively showed off the 3DS graphics but thinking about it I think you'd probably be able to recreate it on DS hardware.