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As a kid:
>GSC Morty
If he managed to pull of that Hypnosis + Dream Eater combo, it was gg. The only thing I could do was to hope for Hypnosis to miss.
>GSC Clair
Fucking Dragonair paralysing your whole team first, after which you're trying to beat that bulky as fuck Kingdra with practically no weaknesses.
Difficult as fuck no matter whether you're a kid or an adult:
>Ruby/Sapphire Norman
Holy shit those Slaking. It's absolutely retarded that if you're not carrying a Blaziken with you (which requires overleveling), you can't even 2HKO those fuckers at that point of the game, while they will 2HKO all your Pokemon (OHKO if you do the mistake of statusing them). Skarmory is pretty much the only Pokemon that can withstand their attacks but it can only 6HKO them at best.
>Emerald Wattson if you chose Treecko
I played Emerald for the first time just a while ago since I only had Sapphire as a kid. God. Fucking. Damn. That was true hell. I never in my wildest dreams had expected that a Manectric could be that bulky. It was the first time in many many years that I actually lost to an in-game trainer. I could just barely beat Wattson on my second try with a little luck on my side. The most difficult battle in the series, hands down. Choosing Mudkip in the beginning of the game however turns the battle into a joke.