I don't recall losing to Whitney at all so not gonna jump on the bandwagon. Norman surprisingly wasn't hard for me at all since my favorite type of pokemon (Ghosts) are immune to a lot of what he throws at you. Tate & Liza were hard in the anime, not in game. Surf rips them to shreds. Heck, a Pelipper could probably solo their fight in Emerald.
Hardest Gym Leader for me was probably Lenora. While Whitney might've had some good power behind her, the sleep condition is absolutely debilitating at that point in the game (unless you blew your cash on awakenings). Combine that with Retaliate, and you've got something to contend with.
Lenora's sleep condition can be neutralized by putting a Chesto berry with your pokemon which was given to you before her gym (I didn't realize that until after I'd beaten her, believe it or not). Though I have to agree that Retaliate was kind of nasty since you were at a pretty low level when you battled her.
I think the gym leaders I had the most problems with were Lenora, Norman in Emerald (barely beat him with my Makuhita), Clair and Morty in HG/SS (barely beat him in HG with a Haunter; leveled up the Giratina I received in Sinjoh Ruins to where it learned Shadow Sneak in SS). Also Fantima in Platinum was a real bear as well.
Leading with the respective Gen and the game I started playing with.
Gen 1 (Red): Brock & Misty were difficult since I started with Charmander, but I could've gotten past Brock easily with Butterfree, but back then I had no idea how everything worked. I always have Pikachu, so Misty isn't all that hard. I can't remember actually losing to the rest, but at the time they were still difficult. I'm picking Misty because if you don't have anything Water is weak to, you're going to have a difficult time. Which means if you don't have Bulbasaur, Pikachu, Oddish or Bellsprout, good luck.
Gen 2 (Gold): Yeah, yeah. Whitney was tough. Rollout was super-effective against my Quilava, and that blasted Attract. I lost about 3 times because I ran out of experience to get from Trainers (I event went on ahead to the Park.) I knew how things worked in this game since I was older and know a lot more about it. But my team was awful in the game: I had Typhlosion, Furret, Dunsparce, Lanturn, Ariados, etc. so naturally they were all going to be very difficult. Pryce was tricky actually, but I played off his extra weaknesses.
However, my pick for this game is Clair. I lost multiple times to her, since outside of Dragon, Kingdra had no weaknesses. I did have my own Piloswine, but it didn't mix well with Water. Her Dragonair(s?) also had coverage. I can't remember how I won outside of trying to level and items.
Gen 3 (Sapphire): Remembering back, this game actually tore me a new one. I lost to Roxanne the first time even though I had Mudkip. Rock Tomb was new and was catching me off guard. Once Mudkip evolved I won. Brawley's Makuhita was awful. I didn't have a Psychic type. I think I maybe had Taillow, but it didn't live. I'm sure i lost once here too. I didn't lose again til Norman I think, but I used items and Truant against him to win. Winona's Altaria was tricky because I didn't know what it was or it's typing, but I still won. Liza & Tate were challenging, but Surf. Wallace's Milotic blew chunks, but again, I eventually took it down without losing.
Flannery is my favorite Gym Leader, but I'm picking Norman. Even with the free turn, if you aren't prepared, he can one-shot your Pokemon. Funny how formidable those Normal types can be ingame, huh?
Gen 4 (Diamond): lol. I barely remember these jokers. I cut through them like a knife through butter. I'm picking Gardenia simply because a 2nd Gym Leader having a thorough final evo that early is ridiculous (and needs to be implemented more.) If we're talking about Platinum, then Volkner, because of that Electivire. But I never lost to any of these.
Gen 5 (White/W2): Lenora wrecked me in the first one. Gardenia syndrome I guess. I think I might have lost, but I'm not sure. Clay can be hard too, as well as the Dragon Leaders, but at this point in the series, having the right types at that point in the game makes them null. That could be said about any of them, though. I'm picking Lenora. Of course she's replaced in the 2nd game. In that case I would pick Drayden, only because of the upgraded team/attacks. No trouble for me though.
Gen 6 (X): lol. I never lost, but I did have some trouble with a few. Clemont spooked me a little with Electric Terrain, and Heliolisk as well because I hadn't looked at any of the new Pokemon or types. He went down easily though.
I'm picking Valerie, simply because I was tripped up a bit by the Fairy type. I wanted to say Olympia or Wulfric, but it was over in 3-4 turns for them.
Still no Dark Gym. :( --- http://gekkoukitsune.deviantart.com/ Fan Art & More PSN: UraharaShoten | Pokemon X: Gekkou - ID: 42323