If I had to pick an in-game moment, I guess I would say Morty's gym. I had a hard time figuring out how to maneuver through the place and even when I did, Morty was a tough cookie. Lost a handful of times, haha. Everyone else complained about Whitney's Miltank and my issue was always Morty's Gengar.
You think Morty was hard for you? Imagine this. You just got into Goldenrod. You had just caught some nice Pokemon on Route 35, but you had also caught this stupid, ugly-looking pig-elephant-thing, that the only reason you even bothered catching it was because you were told to "Catch 'em All". You were going to go check out the Gym, BUT, being the clever little kid you were you decided to go check out the other buildings, talk to people, stock up on a few items. Well, in the Goldenrod Department Store, this guy offers to trade you a Pokemon that you don't yet have in return for the "butt-ugly pig-thing" as you had taken to calling it. Obviously you wouldn't refuse, right? Catch 'em all, after all.
So, now you had just traded that pig for this little dude, not really that cool but a lot better than the pig, and, on a whim, you put him on your team for Whitney's Gym battle. Wow! That little dude is SO TOUGH! He just one-shotted EVERYONE! Even that Gym Leader that your friends say is super-hard! Not only that, but he levels really fast. A lot faster than your other Pokemon. So you think, "Man, this Machop guy is really cool. Let's keep him on my team permanently." So you do that. Not a bad idea, except you put him on your first slot, and barely switch him out for any other Pokemon.
Now your Machop, now a Machoke, has just hit level thirty. Suddenly, he's not listening to you anymore! Oh well, you'll figure it out later. Lets fight the new Gym Leader, Morty... Bad idea. Every single one of your Pokemon is severely underleveled, except for your Machoke, who isn't listening to you! Well, you're not going to stop now! Let's go on! I'll get the levels back off of these creepy old people. WHAT IS THAT!? WHAT SORT OF CREEPY POKEMON IS THAT?! A GHOST-TYPE? WHAT'S A GHOST-TYPE?!?! WHY DID I JUST GET SENT BACK TO THE START?! Ugh, finally at the Gym Leader. WHAT?! THIS MORTY GUY IS TOUGH! Guess I'll just have to hope Machoke listens to me. Go, Machoke! Use Punch Attack!!! WHAT?!?! What do you mean he's sleeping. Come on man! You're getting beat up! Machoke, use Dropkick! WWHHHAAAAATTTTT!?!!?!1?! WHAT DO YOU MEAN IT DIDN'T DO ANYTHING?! MACHOKE LISTENED TO ME AND IT DID NOTHING?! WHYYYYYY?!?!
Repeat until Ghost-Types have become cemented in your mind as the most powerful Pokemon type in existence because it took you LIKE A GAJILLION TIMES TO BEAT THAT GENGAR!!!
That is my experience with Morty.