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The first time around the only leaders that really gave me trouble were Tate and Liza [I had no idea Tate was a boy til I read it on Wikipedia [Random fact for you there :P]]
But the second time around I've sailed through them all. I just took Gym 7 down with Grumpig [Confusion to protect Gyarados] and Gyarados [Surf and Dragon Rage just to finish them off]
Winona and her flippin altaria. That thing destroyed my team. Tate and Liza were hard because I always insisted on using blaziken when I was battling them and I didn't have a dark type. Flannery's torkoal was a little hard to beat, too.
I have no problems with dispatching her Slugmas - They're essentially there to provide EXP - But her beastly Torkoal always puts the brakes on what would otherwise be a full-blown sweep. Unless I started off with a Mudkip or caught a Marill/Numel/Geodude and trained it up some, there is no way in which I can confidently go up against her.
I believe that Liza and Tate deserve a mention, but only their Emerald recreation. The R/S version of Liza and Tate is nothing in comparrisson.
Tate and Liz were the hardest for me. I got sick of my team so I got rid of the one pokemon that could probably take them both on his own and switched him for wailmer (which was always killed by solarbeam before he could do any real damage)
Winona. Her Pokemon aren't much trouble, but her Altaria is impossible to beat. If I use a Rock type Pokemon to use a Rock type move, she 'Quakes me. This thing has never failed to annoy me. Honorable mention goes to Brawly, who I rarely have anything good against him that early in the game. In my most recent Sapphire playthrough, a Zubat just stalled it out (Fighting move on Zubat = divided by 4 resistance). I really haven't ever had trouble with Tate and Liza though. I usually have a Dark type on hand to beat her.
Hmm Winona annoyed me because of her haxy dragon dance boosts with Altaria. Especially when it has earthquake. I found tate and lisa annoying in R/S because they were easily beaten by fishing up two wailmer and spamming surf. Flannery was a little annoying because of attract. The gym leaders were done well in R/S/E I don't have many problems with them in terms of difficulty expect stupid Tate and Liza.
Sadly, Wattson. I always chose Mudkip as a starter and was sonicboom-ed by Magneton the whole time, it took me quite a while to realize that Magneton didn't have levitate. TT_TT