Oh, boy, should I break this down into by generation? Think I will.
Gen I Kanto: when playing with Charmander, Brock and Misty were impossible. But Sabrina was really hard, too. Her Pokemon are level 50 in Yellow.
Gen II's Kanto: none, really, but Blue can be annoying sometimes.
Gen III Kanto: none were really that hard in FR/LG.
Gen II Johto: Whitney, Jasmine, Clair.
Gen IV Johto: Still Jasmine. Her Steelix is level 35, which is higher than Pryce's entire team...Whitney is also pretty hard and annoying. Rollout has destroyed my entire team many times over.
Gen III Hoenn: Wattson's team gave me so many problems as a kid. Norman was pretty difficult in Emerald, and Tate & Liza are devastating in Emerald, as well.
Gen VI Hoenn: I don't remember struggling with any of the gym leaders in or/as, or maybe it's just been too long for me to remember.
Gen IV Sinnoh: God, Maylene's Lucario destroyed me as a kid, I won't lie about it, Fantina was difficult in Platinum, too, and Byron was a bit of a struggle.
Gen VIII: All of them. I don't think I won a single gym battle on my first try in these games except for Roark. Some of the remake versions of these gym leaders had competitive-ish teams which just was too challenging, if you ask me.
B/W Unova: Lenora is really hard if you're not prepared for her. Elesa with Emolga and Volt Switching out was annoying.
B2/W2 Unova: Still struggled with Elesa, tbh, but Clay in challenge mode when I had a Phione on my team was a very difficult battle. I didn't find Cheren, Roxie or Marlon difficult in these games, though.
Kalos: none of them all of these gym leaders suck, period. I only really struggled with Valerie, tbh because Fairy was new at the time.
Alola: "SUN/MOON ARE EASY/BABY GAMES"... Lurantis was the hardest, if not the most annoying and difficult totem Pokemon ever. But, I struggled with all of them. The stat boosts and Pokemon calling for help made it hard for me to even win on the first try. For Ultra Sun/Moon, I struggled with all the totems, as well.
But, the Island Kahunas in comparison weren't hard.
Galar: I struggled with the latter half of the gym leaders here and there, but none of them were extremely difficult? Raihan is up there, though, with his weather teams. He may as well just be "the weather gym leader" instead of Dragon. But, I found him more difficult in the tournament than the actual gym battle.
I have no comment on Paldea as I haven't bought S/V as of posting this.