Where do I start...
G/S/C/HG/SS: Falkner's Mud Slap spamming drove me nuts (doesn't help when you have a Cyndaquil as a starter).
Whitney is a bane of my existance. It takes a miracle to go through her Miltank without some sort of collateral damage. She almost always
flinches you with stomp, leaving you to slowly watch as you white out.
Morty isn't that bad, but come unprepared and Gengar will tear through your team like tissue paper. I always find myself having to sac some of my Pokemon just to win against it, and even then you will be under constant status effects thanks to his Haunter(s).
Clair is an egotist, the fact that she is arguably the hardest gym leader in the game doesn't make anything sweeter. Her Kingdra is demonic in terms of power, only Juan's DTing Kingdra beats hers in terms of annoying; but Clair's Kingdra makes it up for pure, raw power.
SPOILERS BELOW FOR ANYONE PLAYING B/W 2
Cheren can be quite the nuisance, especially when his high-leveled Lillipup appears and repeatedly uses Work Up. Once it gets two or more set up, you are at the mercy of luck and stats; but considering the low levels, you will probably get KOed.
Elesa is just unfair. One word: hax. Her Emolga is the typical Double Team spamming rodent that mops anything you throw at it. Her Flaffy just loves to put you under paralysis. And then Elesa's Zebstrika finishes the job by putting in some Flame Charges which guarantee her the first move.
Clay's Excadrill is OP. Just saying. It is ridiculously fast, and if it gets the chance to get an Attack boost from Metal Claw (which judging by the many complaints here, it will very likely happen), it is GAME OVER.
Skyla is PURE EVIL. The first game she was fine, but now she gets ABSOLUTELY ANNOYING HAX POWERS. Her Swoobat spammed Heart Stamp/Attract and I never got ONE MOVE IN, I WAS FLINCHED TO DEATH. Her Swanna is just a big "f u" to anyone who manages to get to it. It constantly burns you with Scald and lowers your Attack with FeatherDance, making it irritating to defeat her Pokes. And if SHE DOES get you with FeatherDance, she has a Skarmory...which walls everything and sweeps you after using Agility.
Ghetsis is a big troll (although I swept him with +6 Calm Mind Lucario). His Cofagrigus is an amazing staller (unfortunately) and although his Hydreigon is now physical, it doesn't help that he has a Life Orb and good coverage. If B/W Ghetsis made you squirm, then B/W 2 depicts him as Satan. He now holds a Toxicroak that will murder you easily and he has a Drapion and Eelektross that provides more coverage to his already ridiculous team.
Colress in the third battle is just intelligently annoying. ALL OF HIS POKEMON HOLD WELL-PLACED ITEMS AND ARE JUST PLAIN POWERFUL.
Magneton gets much more annoying as it still retains the Thunder Wave/Sturdy trick, but it gets a godsend in the EVIOLITE. Magnezone hits like a tank thanks to its Wise Glasses. Allowing Beheeyem to CM multiple times will spell your doom, and it has Recover so that it can act as a special wall, and Leftovers makes it SO much worse. Klinklang is relatively the same, but allowing it to use Shift Gear a lot is like giving yourself a death sentence.
But he gets two new Pokemon, and this is where the difficulty spikes to ridiculous levels. He now has a METAGROSS AND A ROTOM-W. His Metagross will use Agility and when it starts sweeping, it gets ridiculously powerful. But it is that Rotom-W that makes him difficult. He now HAS A VERY GOOD CHECK TO HIS WEAKNESSES. IT ALSO HAS A LIFE ORB, SO YOU WILL BE LEFT WITH A LOW AMOUNT OF HP, OR BE KOED ENTIRELY. To make it worse, it has Substitute and Will-O-Wisp, which will troll you if you cannot inflict enough damage.