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Johto is very barebones and relies on the idea that every time you got a new HM you'd remember of places you couldn't fully explore and go back to them. Doesn't help that these places are all boring caves
Most of the new Pokémon are babies or single-stage shitmons
More trade-only evolutions - with a twist! You have to trade them while holding limited quantity items!
Only ONE evolution stone of each type. Need to get a Flareon and a Ninetales? Too bad
The game gives you the liberty of taking on Gyms 5-6-7 in any order you wish, but makes it so that there's literally zero level progression between them. The result is that AFTER gym 7 you're still battling trainers with a Lv. 27 Goldeen or a Lv. 28 Pidgey
Level progression remains shit afer the Elite 4 as the Kanto trainers are all hovering around the same level range of the Victory Route trainers (or, the trainers outside of it) to the point that the best leveling up method is still beating the Elite 4 over and over and over again until you can take on Red
Several baffling decisions in Pokémon distribution. Marill is exceptionally rare, Snubbul is found in only one route with a 1% chance of appearing during morning, introdcution of runners, many pokémon, including second gen ones, are found extremely underleveled and in Kanto only. Larvitar is the worst offender by appearing at Lv. 15 only at the end of Mt. Silver
TM list removed useful moves like Ice Beam and Thunderbolt to replace them with moves like Fury Cutter and Mud Slap
