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In upping the difficulty of my own hack, I have learned that that there is no one "best" method. A good challenge is a carefully baked cake that uses a proper mix of all the ingredients you have identified.
These two are effectively the same thing. At the end of the day you are just increasing the stats of the enemy pokemon. The important thing to consider is enemy roster stats in comparison to the player's expected roster stats at any particular point in the game.
Consider trainers in a hack's first mini dungeon (viridian forest or what have you). The player team is going to be early-game basic pokemon around level 5 to 8 with very, very few EVs. If you make enemy trainers there have level 9 to 11 mons with perfect IVs and EVs boosting them to effectively level 12 to 15, then the player is going to have a bad time. It just becomes blatantly unfair to be constantly outmatched trainer after trainer for no reason other than the game's math. The answer is to grind some levels, but grinding levels is merely the illusion of challenge.
This is similar to increasing levels. If you just give better moves to enemy trainers that far outstrip what the player currently has access to then the challenge involved is just to, once again, grind out some more levels.
Okay, so you've carefully balanced every trainer so that their stats and moves are comparable to what the player team is expected to be when encountered. You've even added mons to their teams so that they have the about the same number as the player when everything averages out. Now you have another problem. Those routes and caves full of trainers? They become a massive slog!
Imagine every lass, youngster, and hiker fight being one where your teams suffers a KO or near-KO and the rest of your roster is hurting for HP. The player, whilst tearing their hair out, is going to be running back to the pokemon center unless you make healing items much, much more plentiful. That is why vanilla games keep regular trainers mostly at 2 or 3 pokemon. It's just enough to wear the player down little by little with each trainer fight. Ideally you want to have the player come out of that area barely hanging on but victorious. You want a gauntlet, not a death march.
Adding pokemon to enemy rosters can also work against difficulty. Each new trainer mon is a new source of boosted exp. Adding one or two mons to every trainer in the game can easily cause the player's team to over-level beyond expectation. Note that this can be done intentionally in order to rectify dead zones in the game where the player seems under-leveled and has to grind low-level wild mons (*ahem* looking at you Johto region).
Less of a challenge and more of way to break up stagnation. Do these in long stretches of trainer battles to keep things from getting boring. But don't overdo it. Moderation helps keep it special and interesting.
This is trying to fix a flaw in the game by forcing the player to play a certain way. I'm just going to out and say it. This is bad game design, it should be avoided, and is really just unacceptable.
I'm going to call out a specific example here with Gen 8 since it really illustrates my point. Sword and Shield flat out prevent you from capturing pokemon that are too high a level unless you have the right badge. The reason is because high level pokemon can spawn in the open wild areas, and it would break the game's progression if you could catch them. But that is a poor excuse for bad game design. A proper solution would be to have different encounter tables for each wild area based on how many badges the player has. This way the player never encounters wild pokemon that would break progression while also giving the player a reason to return at various points in the game to see what has changed.
Pokemon games generally have three "groups" of AI opponents.
I'll say it again. You don't want to turn your routes and caves into frustrating slogs. You need to have a good mix of trainer AI to prevent every trainer from being the same super-elite every 20 steps. It gets samey, dilutes the feeling of player progression, and takes away from the excitement of fighting the gym leaders. Use trainers from the first group as a warm-up; let the player feel their growing strength by smashing a few nobodies into the dirt. Then up the ante with some trainers from the second group, and intersperse some trainers from the third group throughout in order to keep players on their toes. Finish off with a one or two tough fights to act as a mini-boss (the SS Anne rival battle is a perfect example of this).
I'll close by stating this. Making a proper challenging pokemon game isn't about taking one aspect (like raising levels) and applying it across the board. Pokemon game difficulty is actually carefully calibrated. Albeit the whole issue is that it is always calibrated to be difficult for an easily-distracted 9-year-old. Making them more challenging for teens and adults means going back, understanding all the subsystems, and re-calibrating the whole experience for an older audience.
1. raising the level for every trainer pokemon for every battle encounter.
2. boosting their evs/ivs.
These two are effectively the same thing. At the end of the day you are just increasing the stats of the enemy pokemon. The important thing to consider is enemy roster stats in comparison to the player's expected roster stats at any particular point in the game.
Consider trainers in a hack's first mini dungeon (viridian forest or what have you). The player team is going to be early-game basic pokemon around level 5 to 8 with very, very few EVs. If you make enemy trainers there have level 9 to 11 mons with perfect IVs and EVs boosting them to effectively level 12 to 15, then the player is going to have a bad time. It just becomes blatantly unfair to be constantly outmatched trainer after trainer for no reason other than the game's math. The answer is to grind some levels, but grinding levels is merely the illusion of challenge.
3. programing different move sets.
This is similar to increasing levels. If you just give better moves to enemy trainers that far outstrip what the player currently has access to then the challenge involved is just to, once again, grind out some more levels.
4. adding more pokemon to each trainer.
Okay, so you've carefully balanced every trainer so that their stats and moves are comparable to what the player team is expected to be when encountered. You've even added mons to their teams so that they have the about the same number as the player when everything averages out. Now you have another problem. Those routes and caves full of trainers? They become a massive slog!
Imagine every lass, youngster, and hiker fight being one where your teams suffers a KO or near-KO and the rest of your roster is hurting for HP. The player, whilst tearing their hair out, is going to be running back to the pokemon center unless you make healing items much, much more plentiful. That is why vanilla games keep regular trainers mostly at 2 or 3 pokemon. It's just enough to wear the player down little by little with each trainer fight. Ideally you want to have the player come out of that area barely hanging on but victorious. You want a gauntlet, not a death march.
Adding pokemon to enemy rosters can also work against difficulty. Each new trainer mon is a new source of boosted exp. Adding one or two mons to every trainer in the game can easily cause the player's team to over-level beyond expectation. Note that this can be done intentionally in order to rectify dead zones in the game where the player seems under-leveled and has to grind low-level wild mons (*ahem* looking at you Johto region).
5. changing battle type. (like more double battles or rotation battles)
Less of a challenge and more of way to break up stagnation. Do these in long stretches of trainer battles to keep things from getting boring. But don't overdo it. Moderation helps keep it special and interesting.
6. setting level caps through exp gain adjustment.
This is trying to fix a flaw in the game by forcing the player to play a certain way. I'm just going to out and say it. This is bad game design, it should be avoided, and is really just unacceptable.
I'm going to call out a specific example here with Gen 8 since it really illustrates my point. Sword and Shield flat out prevent you from capturing pokemon that are too high a level unless you have the right badge. The reason is because high level pokemon can spawn in the open wild areas, and it would break the game's progression if you could catch them. But that is a poor excuse for bad game design. A proper solution would be to have different encounter tables for each wild area based on how many badges the player has. This way the player never encounters wild pokemon that would break progression while also giving the player a reason to return at various points in the game to see what has changed.
7. or changes to the AI.
Pokemon games generally have three "groups" of AI opponents.
- The first is the know-nothing trainers that choose moves totally at random. Usually given to youngsters since they are supposed to be very young children, and to cueballs since they are rather unintelligent.
- The second is amateur trainers who avoid making dumb decisions (using sleep powder on a poisoned pokemon, trying to double-confuse an opponent, etc) but also don't use strategy like STAB, type-countering, or making proper use of movesets. These are your trainers like bugcatchers, rockets, bikers, and blackbelts.
- The third is professional trainers who know what they are doing. They do everything from the second group but also make use of the type chart and movesets. These are your leaders, ace trainers, jr trainers, and rivals as well as trainers like gentlemen and sailors.
I'll say it again. You don't want to turn your routes and caves into frustrating slogs. You need to have a good mix of trainer AI to prevent every trainer from being the same super-elite every 20 steps. It gets samey, dilutes the feeling of player progression, and takes away from the excitement of fighting the gym leaders. Use trainers from the first group as a warm-up; let the player feel their growing strength by smashing a few nobodies into the dirt. Then up the ante with some trainers from the second group, and intersperse some trainers from the third group throughout in order to keep players on their toes. Finish off with a one or two tough fights to act as a mini-boss (the SS Anne rival battle is a perfect example of this).
I'll close by stating this. Making a proper challenging pokemon game isn't about taking one aspect (like raising levels) and applying it across the board. Pokemon game difficulty is actually carefully calibrated. Albeit the whole issue is that it is always calibrated to be difficult for an easily-distracted 9-year-old. Making them more challenging for teens and adults means going back, understanding all the subsystems, and re-calibrating the whole experience for an older audience.