Johto stands out as the only region in pokemon history that is not 100% linear. Once trainers have obtained the Surf HM, they are technically free to roam either east to Mahogany Town or south to Olivine City. However, do trainers make use of this freedom? More often than not, they don’t.
Based on the order of the badges, most trainers head south, all the way to Cianwood City to defeat Chuck, then north to challenge Jasmine and finish in Mahogany Town. It turns out there’s a much better way to go about things with a more streamlined level progression. Trainers should definitely try to optimize this part of the game, whether they’re doing Nuzlocking or just trying to beat the Elite Four.
The problem with traveling through Johto in the usual way is that Pokémon will seem vastly undervalued when trainers reach Mahogany Town. The same can be said for the Gym Leaders — Jasmine’s Steelix is an elevated level 35, while Pryce’s strongest Pokémon is his level 31 Piloswine (raised to level 34 in Heart gold and soul silver). Since that’s the case, does it make sense to fight Jasmine before fighting Pryce?
Then, of course, there’s the general level difference of Pokémon between the two areas. After defeating Morty in Ecruteak City, the trainer’s team should go to level 25. However, if they go west, into Mt Mortar, they will eventually find level 13 Machops and Zubats. The opponent’s trainers also have under-leveled Pokémon, most of which hover around level 17.
This can be very frustrating when playing any of the Johto games. Since trainers usually beat Chuck and Jasmine before they even set foot in the mahogany town, that means their party will be around level 30 by the time they actually arrive. As a result, these trainer battles will all be laughably easy, and those Pokémon will gain little to no EXP from winning those battles.
Nowhere is this problem more painfully evident than in the Team Rocket showdown at the Mahogany Radio Shack. Trainers here will have to slog through a room filled with low-level Team Rocket Grunts, all of which appear to have level 17 Zubats, Drowzees, Rattatas, and Grimers. If you’re forced to deal with these opponents with level 30 Pokémon, the game will just slow and annoyingly grind to a halt.
Is there a way to make this less annoying? Well, luckily there’s a better route in this part of the game, one that won’t feel so frustrating. The best thing a trainer can do after getting the Surf HM is head west to Mahogany Town. From there, take out the enemies in Mt. Mortar, travel to Lake of Rage and head to the Mahogany Radio Shack for the Team Rocket Mission.
This does several things. First, Trainers can clear these low-level Pokémon before their own team starts reaching level 30. Second, it’s smart to pick up the Lake of Rage Gyarados at this point in the game, as it does well against Chuck’s Poliwrath and Jasmine’s Steelix. Plus, trainers will gain stronger teams when they go up against Jasmine, who can be one of the tougher Gym Leaders in the game (especially if Steelix hits his Iron Tail).
After defeating Team Rocket at their HQ, it’s best to ignore Pryce’s Gym for now and head west to Olivine City instead. The opponent’s trainers in the lighthouse have Pokémon from about 22 to 24, so it’s better to beat them after the Team Rocket mission.
From there, trainers can head to Cianwood City to beat Chuck, as they should have a team that’s around 27 to 30 at this point. Once Chuck is dealt with, Trainers must fly back to Mahogany Town, defeat Pryce and heal Amphy. Then they can challenge Jasmine.
Unfortunately, this does not solve all leveling problems in the Johto region. The Pokémon found after Blackthorn City are still very underrated, as are most in the Kanto region. However, the idea behind this optimal route is to give trainers a bigger edge in the endgame. Nobody wants to fall behind on levels going to Blackthorn City Gym because that means they are guaranteed to be below level when they go to the Elite Four.
Trainers still often play the Johto games, especially Heart gold and soul silver. These are also popular games for Nuzlocke as trainers want to look for every little optimization they can find. Nuzlockers in particular may want to try going through Johto with this optimized route as it ensures they never fall below the level of a major battle.