Whitney is definitely the most obvious, because you don't get much coverage options for her at the point you get to her, plus Miltank has a deadly combination of Attract (to badly ruin male opponents), Rollout (gets stronger every hit), Milk Drink (self-healing) and Stomp (chance of flinch which is bad given it's not as slow as you'd think).
Norman and Lenora are also no slouches either. Norman has the deadly Facade strategy, and both Lenora and ORAS Norman have Retaliate which hits extremely hard at the point you're at them. Norman's Slakings are also one of the reasons why he is insanely difficult.
Clair is also hard, because Kingdra is only weak to Dragon and that's a type you'll unlikely have on you by the time you face her. Doesn't help she's also got a Gyarados and two annoying Dragonair who can wreck hard.
And of course, Elesa. In B/W she's much harder thanks to her Emolga duo who are fast and can't be damaged by Ground-type moves, plus Zebstrika is extremely fast (in fact faster than anything else you'll likely have) and hits very hard. At least you are able to get the TM for Rock Tomb which is able to handle the Emolgas.
Fantina in Platinum is also really tough for a 3rd Gym, and that's due to her Mismagius having insane type coverage for that early stage of the game (she has Ghost, Psychic and Grass-type coverage along with Confuse Ray). Duskull and Haunter also love to mess with you badly.
Cheren in B2/W2 has to be one of the hardest 1st Gyms, because if his Lillipup gets the deadly Work Up + Tackle strategy rolling, expect to be creamed. You can get a Riolu, but it doesn't learn a Fighting move until Level 15, which is hard to get to without Audino grinding.