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I'm curious, and I want to start a nuzlocke on the hardest main series Pokemon game (in general). Which game has the hardest gyms, elite 4, and Pokemon to capture/obtain OVERALL

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It’s fine, cleared flags.
So how do you think we should measure "hardness" in Pokemon games?
@sumwun By the Most trainers, highest levels, and with the most high catch rates respectively.
And trainer's AI?
yes, rahat.

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If we're measuring this by levels, then the hardest games are HGSS with that level 88 Pokemon #025.

Every Pokemon game is very easy if you just choose either the fire or water starter, make it use its strongest move during every turn, and catch a new HM slave whenever you need it. Because of how experience works, a Pokemon game is difficult only if you want to train more Pokemon, so you can make any game as difficult as you want by changing the size of your team. I think a good way to compare different games' difficulties is comparing how difficult they still are when players are using only one battler (and otherwise trying to make the game easier), and this is basically a speedrun.

USUM: 5:36
SM: 5:01
SwSh: 4:05
XY: 3:43
DP: 3:33
Pt: 3:27
HGSS: 3:27
BW: 3:13
BW2: 3:12
GS: 3:10
C: 3:10
ORAS: 3:05
E: 2:26
FRLG: 2:01
Y: 1:54
RS: 1:53
RB: 1:46
source
Then again, the fact that USUM are at the top is probably more because of the annoying cutscenes that you can't skip than it is because of difficulty. Please tell me if you come up with a better way to measure the difficulty of a Pokemon game.

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I'd have to go with Pokemon Diamond and Pearl

Diamond and Pearl is really the only main series Pokemon game I've played where I had to actually train to be on par with the normal NPC trainers throughout the game. And as for the Elite Four and Champion, pretty much all of the elite four's levels are in the high 50s and low 60s, when the rest of the games have their elite four's levels barely approaching 50. Kanto, Unova, and Kalos' elite four are an exception to this.

However in Kanto, your levels seem to be a lot higher when challenging the elite four. In Unova, you have access to insanely powerful Pokemon such as Coballion and Volcarona that can completely sweep every member by themselves. And in Kalos/Alola, the new exp share made it ridiculously easy to gain exp for your Pokemon, making your Pokemon completely overleveled.

And now meet Cynthia, the single most powerful and unfair champion in Pokemon. She has six actually competitively viable Pokemon with movesets and typings that compliment each other well, and covering up their own weaknesses (aside from mirror coat on Milotic). Her team's levels are already in the 60s when your team's levels are somewhere around 50-55. And her Garchomp? Level 66. To beat that thing I was forced to be cheap and use my Palkia and give it a few extra levels with all the rare candies I had. Her Garchomp also holds a Sitrus Berry so if you think you've got it down low, it chomps down that berry and restores it back. Yes, ice moves are super effective on Garchomp. But you're not outspeeding that monster is the problem, it'll hit you first. And make no mistake, it'll definitely kill you with the STAB dragon rush and earthquake it has. And if you even dare bring out an ice type, it's got brick break for that. I lost to the elite four several times and lost to Cynthia more than can be counted. God I hated her.

I personally had the most trouble with Diamond and Pearl because of the overleveling issues with trainers and the elite four, as well as the mediocre exp share. The Pokemon you can get were pretty limited with no really powerful ones available before challenging the elite four and to top it off Cynthia made it near impossible to finish the game with her overpowered Garchomp.

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If you like the answer then you should click the green check mark at the top right corner.
Also, having played the two games right before and right after DP but not DP themselves, I think this answer might be a bit exaggerated. First and foremost, the experience gaining and level gaining mechanics absolutely did not change at all between Generations 3 and 4. I don't know who said it did.
If Volcarona can easily sweep every Elite Four member in BW2 by itself with an 85% accurate fire blast, then Infernape and Staraptor can do it even more easily in DP. I know Cynthia is stronger than she is in Pt, but if you call dragon rush and giga impact "competitively viable" then you aren't playing enough competitive. If your team was around level 50 when you battled her, then that means you either used too many Pokemon or didn't battle enough of the trainers in the optional areas. So you can only blame yourself for that. And just because ice type moves are good against Garchomp doesn't mean you need an ice type Pokemon to use them. An ice beam Floatzel works great. It even outspeeds her Garchomp. Also, I don't know why you think there are no powerful Pokemon available before challenging the Elite Four. If Infernape and Staraptor aren't good enough for you, then I don't know what is. I'm pretty sure DP had better Pokemon than all the games before it, mainly because of damage categories. Back in GSC, the strongest Pokemon was Feraligatr, a physical attacker with no physical STAB. Generation 3 was a little better, with Swampert being ground type and Blastoise having good special attack, but they were both a little slow. All the fast starters, the fire types, had to wait until their level 30's or 40's to learn fire attacks that weren't ember. And in DP you have Chimchar, with amazing stats in speed and both attacks and learning both fire blast and focus blast before the 3rd gym. DP also introduced Starly, probably the most broken non-starter at the time. Sure, Spearow was great in GSC, but its best flying attack was peck until you get the HM02 fly. Starly learns wing attack almost right after it's caught. Then it goes on to learn both close combat and brave bird by leveling up. The addition of damage categories also helped a bunch of old Pokemon, like Gyarados. So maybe DP was harder than the other games, but I don't think the difference is that much.
@sumwun, i would've clicked the green check, however i just saw this and realizing that your comment* is much more stronger and detailed.
Sorry, I didn't mean to start an argument or anything. After reading your comment I don't think the lack of good pokemon is a reason for making the game difficult anymore. However, I'd say that in GSC (I never actually played crystal so I'm not actually sure how much different it'd be) it was a lot easier for my pokemon to level up because exp gain wasn't on an exponential curve like DPP was. Thanks for correcting me though, guess I just had a crap team in my playthrough of Pearl and Platinum.

Another thing - I used flamethrower with Volcarona, not fire blast. The exact moveset was bug buzz flamethrower psychic and quiver dance. I didn't sweep ALL of the elite four, maybe around tenish pokemon before my others took over. Also, in my playthrough of Gold I actually chose Meganium, but managed to do fairly well against e4/champion because I'd say Ho-oh and Alakazam are stronger than Feraligatr.
No experience curve was ever exponential. What are you talking about?
Also can you maybe edit your answer?
–2 votes

HeartGold/SoulSilver is probably the hardest, but only if you play through the entire game. The Gym Leaders/Elite Four/Lance are pretty easy, but when you fight Red at the very end, you have to deal with a level 88 Pokemon. Diamond/Pearl is also pretty hard, since everything is high level.

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HGSS is definitely easier than GSC. You can't find a level 50 Magikarp on Route 43 in GSC.