The first time I played, I struggled a lot during the battle against Brawly and Tate and Liza... then when I reached the last gym (probably Juan), an overpowered Kingdra was there with Ice Beam and Earthquake (pretty much wiping everything that stood a chance against it).
On a recent mono-type of Emerald, I've discovered that Wattson is a nightmare when you have no Ground/Fire-types, and don't even get me started on Flannery without Water-types. I have no idea how I managed to beat her- I think it was just on account of dumb luck. (It probably was- her Torkoal's Overheat missed two turns in a row and it wouldn't have lasted another hit from Mightyena's Dig.)
I had thought Brawly would be tougher than he was, but I sent out Sableye and that made him stupidly easy, actually.
The fact that I chose Treecko as my starter made Winona a formidable opponent. Winona's Swellow, Pelipper, Skarmory, and Altaria was a well rounded team in the Ruby and Sapphire games. Her team was so annoying due to the fact that she tried lowering your Pokemon's accuracy with Sand-Attack, confusing them with Supersonic, and using Dragon Dance to give Altaria the opportunity in dealing heavy damage thanks to its boosts in Attack and Speed. Fortunately, I had a Manectric that came in clutch when dealing with Winona.
Wattson was probably the hardest for me, especially with his Magneton with the occasional Thunder Wave slowing my 'mons down. It took me about seven tries in order to beat him, and my Lairon single-handedly KO'd the Magneton with Rock Smash. It took a lot of grinding for me back then.
It took me FOREVER to beat Juan the first time, with Flannary actually being slightly difficult despite my choosing mudkip as my starter (stupid attract!)
Tate and Liza proved to be much more formidable in my most recent run, though. The freakin' claydol kept using earthquake to take out my lairon, and solrock's solar beam made quick work of my swampurt.