Misty's Starmie was tough.
Lt. Surge's Raichu was tough.
The rest became easy over the course of the game.
Misty's Miltank, with that flawless Rollout combo that hit unless you had Double Team.
Claire's Kingdra was a pain as it was a Water/Dragon meaning neither Ice or Electric was super effective.
Watson's Magneton took way too long to beat. The fact it kept trying to paralyze then Shock Wave did not help.
having an Aron/Larion or Geodude/Graveler helps
Tate & Liza's Lunatone + Solrock combination was very hard to beat. Thankfully they were made a little easier in Emerald.
Wallace's Milotic, it using Recovery constantly was very annoying.
Crasher Wake's team gave me some problems and was rather tough given I had Lopuuny, Gardevoir, and Prinplup on hand.
And Whitney is still tough....
in my opinions, all those gym leaders were rather tough/difficult to beat