Kanto: I think Sabrina was hardest for me for two reasons: I thought you were supposed to defeat her before Koga until recently, and there are no Dark types in Kanto to troll her with. I don't think she ever gave me too much trouble, though.
Johto: Clair was hardest because, like with everyone else, I couldn't find anything to exploit her weaknesses. In my most recent run of SS it was slightly easier since I had a Dragonair that I bought from the Game Corner, but Dragon Pulse hit me harder than Dragon Rush hit her.
Hoenn: Wattson does give me occasional trouble because the only Ground types I can find before him are Marshtomp/Swampert and Nincada, the first of which I don't always pick and the second of which is horrible. I thought I could just whittle him down recently in Emerald with Shedinja, but he always hits with Supersonic and I always hit myself due to hax.
Tate and Liza were pretty easy in Ruby and Sapphire, but the addition of Xatu and Claydol in Emerald made them abso-freaking-lutely horrible. What especially gets me is that they're about 5 levels higher than everyone else in the game at that point. I just beat them earlier today; the gym trainers were in the mid-30s, they were at low-40s, and completely over-powerful. Fortunately, I got Gardevoir to set up 6 Calm Minds to wall everything they threw at her, stall them out to the point where there were no more offensive moves on Xatu and Lunatone (somehow got rid of Claydol), revive Sceptile and Leaf Blade/Psychic combo everything. They were evil and I wish video game characters could die horribly so I could crap on/in their graves (even though they're children).
Sinnoh: None of them were really challenging for me as far as I can remember. I guess Byron was a little more difficult because his Pokemon are so defensive, especially Bronzor/Bronzong. I hate Bronzong in any situation because it is just the most annoying Pokemon ever.
Unova: The gyms here were pretty easy for me, even Elesa, who apparently everyone else had trouble with because they did not own an amazing Palpitoad like me. In all honesty, the first gym was the hardest for me solely because I hate the monkey trio. They're not too difficult to take down, especially at low levels, but I just hate them as Pokemon. I chose Snivy as my starter, so I got to battle Chili, and unfortunately I received a Panpour, which is my least favorite of the monkeys. I hate Panpour and Simipour, and the only reason why I ever put it in my party after that gym is to use it as an HM slave for Cut. And that is the only problem I had with any Unova gym leader ever.