I've got a couple. Roselia, mainly because my being a swampert trainer in Sapphire makes any grass type encounter cause me to shudder inside, plus its draining moves and ingrain and poison point make it a pretty deadly stall-fighter, at least on the 1-player playthrough level. Also bronzor/bronzong, as it seems no matter what I throw at it, it always just has the result of trying to punch a metal shield. Plus, Bronzy the bronzor was always a pain to play against in contests as well.
You mean that lady on Route 21 near Fortress City and Scorched Slab in Omega Ruby. I'm glad i used Blaziken. I saw a certain pokemon run with only a Castform. This area constantly rains on the overworld, it can't be stopped by Sunny Day and that Roselia and other grass types are a death sentence and so many retries.
A lot come to mind including
Whitney's Miltank- That thing can ruin a good day because of it's notorious moveset. and Don't try to use status on it because Gamefreak snuck a Lum Berry and it has Scrappy Ability. It's way too good in for a early gym in Heart Gold and Soul Silver.
Team Galactic Cyrus- His whole team in platinum, including how often he gets critical hits. His Gyarados knows Ice Fang if you have a Staraptor. His very fast Crobat will use Toxic. and his Weavile is ridiculously fast.
Elesa- Those Volt Switch shenanigans can trip you up if you don't have a Sandile to level up.
Elite 4 Kahili in Ultra Sun- Her Flying type Braviary having Sheer Force and a fleeing move with U-Turn makes this hard hitting eagle unpredictable. Almost underestimated her since i had no electric type.
Totem Marowak Ultra Sun- I kept getting the dances wrong, had to fight more often.
Totem Ribombee- Blissey didn't appear but the Quiver Danceboosts Ribombee gets are absurd in 2 turns. Had to back out and use Toxic on my Mimikyu and basically stall the whole fight out with Max Potions. Then i could beat the others