[Partly biased from my own experiences, but most of us can relate in some way to struggling with these. Comment your personal toughest battles. Let's all talk about how frustrated we got as small children, and even now as competent human beings.]

This list only includes main series battles, otherwise I'd have to list every boss fight from Pokémon Mystery Dungeon Explorers of Sky.

#5 V.S Hau
Pokémon Sun and Moon and Pokémon Ultra Sun and Ultra Moon

I really wanted to put one of the new fights on here, so I think y'all can agree that Hau was either stupid easy or randomly difficult. I didn't put a specific encounter because I remember some instances where my friends and I had an easy time with his Alolan Raichu, while other times, the pancake surfer mouse wiped our entire team. His difficulty range is unpredictable and kinda depends on random luck. Either way, he was still a good rival.

(The most aggravating part about him is how in certain occasions he won't re-challenge you after you lose, so you have to sit with the loss forever.)

#4 V.S Gym Leader Elesa
Pokémon Black and White

This fight is obnoxious mainly because she has to Emolga, which are only weak to rock or ice type moves, both Pokémon that weren't exactly all over the place. (You know, unless you like Roggonrola.) Both knew volt switch, both had static, and finally the Zebstrika had flame charge. Somehow, you'd get paralyzed, and then they'd volt switch until they'd kill ya. Don't think about using that ground type move on the Zebstrika because it'll just volt switch out since it's faster and the Emolga will take no damage. Annoying. This was so annoying to me as a small kid. (In Black and White 2, they gave her only one Emolga, which really made the whole affair a lot easier.)

#3 V.S The First Gym (If Wrong Starter Pokémon Is Chosen)
In These Games Specifically: Pokémon Diamond, Pearl, Ruby, Sapphire, Red, Blue, Yellow, Gold, Silver, Heartgold, Soulsilver, Black, and White. 

I did not include games like X and Y, Alpha Sapphire and Omega Ruby even though the type disadvantage is still there because those games sorta dumbed it down and made it a lot easier. Black and White 2 have a normal type gym leader as your first, so there's no type disadvantage either. However, if you chose a fire starter when the first gym is a rock type, too bad, you'll be either loosing or catching a random Pokémon you'll use once and ditch to the PC box, unless you really like it. Or perhaps you chose Grass when the flying type gym leader is staring you down, and the only rock type available is a stupid Geodude that you refuse to use. (That was me, and I lost at least fourteen times until I just caught a bunch of level five Pokémon to use.)

Most of us have at least had one win streak destroyed by gym one in a Pokémon game.

#2 V.S The Elite Four and Champion
Pokémon Diamond and Pearl

A lot of people will say that Cynthia was the toughest part about Pokémon Diamond and Pearl, but honestly, the entire league is a nightmare. This entry on the list encompasses all the members.

(Except the first bug type guy. He's a cakewalk.)

Seriously though. The gap in levels from the last gym leader to the elite four was a whole ten levels. In fact, on my first playthrough (Diamond was my first Pokémon game) I never completed it because I could never make it past the fourth elite four member. I eventually came back many years later and completed it, but the frustration still stings. Most of the elite four members (apart from the bug dude) have Pokémon that don't exactly match the type theme they have going. (The fire guy has a Drifblim cuz it knows Will O' Wisp. Wow.) By the time I made it to the fourth member, I had normally ran out of Potions, and my Pokémon were practically fainted. We don't need to elaborate on why Cynthia was a nightmare except that I thought her Milotic was more of a nuisance than Garchomp.

#1 V.S Champion Diantha
Pokémon X and Y

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That's a joke.

X and Y is easy.

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HONORABLE MENTION! V.S Gym Leader Whitney
Literally in any game. There's no escape.

Stupid Miltank. Stupid Miltank. Stupid Miltank. Stupid Miltank. Stupid Miltank. Stupid Miltank. Stupid Miltank.Stupid Miltank.Stupid Miltank.Stupid Miltank.Stupid Miltank.Stupid Miltank.Stupid MiltankStupid MiltankStupid MiltankStupid MiltankStupid MiltankStupid MiltankStupidMiltankStupidMiltankStupidMiltankStupidMiltankStupidMiltankStupidMiltank
StupidMiltankStupidMiltankStupidMiltankStupidMiltankStupidMiltankStupidMiltank

It's not number one because that would be too obvious. 

HONORABLE MENTION! V.S Any person in real life that plays as much as you do
Any game

If you have a sibling and a friend who actively plays Pokémon like me, you've probably battled them before. Good guess says you've both won or loss your fair share of battles, which means that since you don't always win, your opponent is a tough one. (Or maybe they're that kid that uses six legendary pokemon while you don't because you have principles. That's a toughie.)

Pokémon is a game all about connecting, so these fights are my personal favorite battles.

#1 V.S Pokémon Trainer Red
Pokémon Heartgold and Soulsilver

This battle is like a rite of passage for any true 100% Pokémon fan because it is officially the highest level trainer battle the Pokémon company has yet to craft. 
The music, the fact that you have to climb a friggin' mountain and beat the Pokémon League a second time on harder difficulty after collecting 16 badges, and the trainer himself make this fight a grand culmination of Pokémon. 

So, the battle is tough because one, the high levels, two, the hail, and some of Red's Pokémon resist the hail, and finally, the team itself. His Pokémon are tough to beat because they cover each other's weaknesses, and there's no true weak link. (It would the Pikachu, but they compensated by making Pikachu extra levels above every other Pokémon on his team.) Snorlax, Charizard, Blastoise, Lapras, and Venasuar are all incredibly tough opponents alone, and it is an exhilarating battle that I barely won after countless revives and potions.

Seriously, speed run HG/SS if you haven't fought Red yet just for this battle. The one in Pokémon Sun and Moon is not even close to this difficulty. 

[A/N: Thanks for reading! Please vote and recommend this story, because these lists are really fun to make. Some lists coming up are top 5 pokemon music themes and ranking all the core series games (remakes included) in a huge list. I guess you could request which one you want to see first more.]