This isn't a specific reply to anyone, but I am going to have to address some commonly asked questions, including the movesets of 247 Pokemon that were modified in some way.
Not all pokemon are created equal. Magcargo and Typhlosion are proof of this. Clearly one is better than the other, and nobody would want to use the inferior one. How could Magcargo compete? By getting better moves earlier.
Pokemon Go introduced a concept of capturing brand new pokemon to replace the old, and it is the only way to do well in that game. Pokemon Crystal Kaizo does a similar thing; (that came before the app ironically), it encourages you to catch newer, fresher Pokemon with better movesets. Wild evolved forms with good default movesets help immensely, and often, single stage pokemon can eventually learn the most advanced moves they could possibly get, such as Heracross, where it eventually becomes one of the greatest pokemon a player could have in Crystal Kaizo. For the difficulty scale, some moves take longer to learn than others. Again, Magcargo vs Typhlosion, the game encourages you to use different pokemon than starters. Its sad that you have to replace some pokemon, but on the plus side, it reduces level grinding that even the original games still have major issues with.
If you really want to keep using the pokemon you caught, you'll have to be patient when they are learning moves. Most moves like leer, growl, tail whip, defense curl (moves that the AI cannot use effectively no matter what subroutines are done) have been removed so that the default sets have mostly attacking moves. The problem is that some pokemon, like Houndoom, movesets don't have additional attacking moves between the filler support moves. It learns Crunch at really high levels.
Fun fact, the original GSC game's rhydon and Golem doesn't get a rock move stronger than rock throw. And lets not go into the horrible learnsets in the original RBY. Leer, tail whip, and rage Tauros anyone? It will take some time to learn new moves for older pokemon, while you fight the weaker pokemon with strong moves, while the boss fights have more powerful pokemon with strong attacks.
That's why TMs are available for use. Goldenrod City gives TMs from the Casino to the Department store, as a reward for winning battles. Fire types with fists can learn fire punch, and some can even learn thunderpunch. Exploration is key.
As for the annoyance from the game? This is not some "slightly harder" mod of the original. This is a Grade A "Nintendo Hard" mod of the game. Encountering annoying strategies is inevitable; many of them are competitive play strategies after all. Gamefreak gifted certain pokemon with event moves; like Pikachu with surf for example. I hear some of complaints that "the game isn't hard, its annoying!" As if its unfathomable that a game could get challenging enough that it could also be annoying.
The player has his or her advantages (Badge Boosts, previewing enemy pokemon, immediate switching, catching any pokemon they encounter, changing rosters before battles, hundreds of healing items) that the NPCs lack, while the NPCs have their own few advantages (every NPC has the best default sets they could possibly have, apart from the complete dud that is Delibird).
"Why is a Psychic type doing in a Poison Gym?" Ask Gamefreak why Kadabra is present among the NPCs in Koga's gym. Or fighting types in a Ground type gym. Or Venomoth in Sabrina's roster. Lots of questions like that.
And its not anything really new. The boss has pokemon with moves you don't have? Just like in the original GSC, or even RBY. Misty has a Starmie; you can't get starmie until you get surf. Lance's Aerodactyl had Rock slide in GSC as well. Ad infinitum.
And for the more legitimate complaints, some map designs. They are really just annoyances from the original games taken to a higher level. Unavoidable grass in a pokemon route? That would hold more water if every beginning town in every original pokemon game didn't force unavoidable grass without repels. Or caves without repels. Like in the original games, you just gotta press forward, and be prepared for the next route.
Cerulean City had no convenient exit in the original RBY; the two exits came from a shrub blocking the way, and a hole in a wall that a criminal made. In-universe, no one could get the surf HM at the Safari Zone in the original RBY. Some map areas are claustrophobic, just like in real life streets. Yes, real life streets and routes leading to dead ends do exist, as hard for you to believe that happens.
And the original game does force you to use HMs until they stop putting obstacles; you still can't remove the HM move until you reach the move deleter (unlike RBY where you are stuck with it forever). The "challenge" of the HMs comes from decision making; do you have strong pokemon that uses HMs that you use through the whole game, or do you swap in HM users with stronger battlers? Its nothing new in Crystal Kaizo; all of the original games force you to use "HM slaves. Even bosses like Lt. Surge and Erika force you to use Cut users. Does it excuse the HM usage? No, so treat them like "kaizo traps" to defuse, and make sure you have good pokemon with weaker movesets that can use an HM.
Does that add to difficulty? Not really, just being consistent like the original games. However, the rosters of every single trainer in the game, including default sets, do contribute drastically to the difficulty, and they use whatever moves they can use to win. The disabling of revives during battle also increases the difficulty, you can't lose certain pokemon, or you could lose the battle, just like in wifi.
A lot of people that "lecture" me about "tedious =/= difficulty" do not understand the real life concept of "penalties." Backtracking is a punishment for those ill-prepared, just like losing a battle, and the HM obstacles and long routes and caves are intended to discourage such failures.
Sure its inconvenient that you have to go underground in Goldenrod, but its technically safer; you can't run across the tracks of a high speed train after all. You can ride your bike underground at least, and it helps with egg hatching, and you can access a PC downstairs. Its slightly longer length as the above ground in the original. Also, the basement in Goldenrod's pokemon center will help immensely with egg hatching due to sheer length.
Most of these obstacles are so that you have to fight trainers, which give off money, experience points, battling practice, locations of newer wild pokemon, and an idea of what level you should be. Gauntlets are important since the end bosses are a massive and very difficult gauntlet.
Next Pokemon Kaizo hack will tone down the map edits and HM usage though. Documentation is currently underway in the planning stage. I already lost documentation for the previous Kaizo hacks due to a hard drive corruption, and I'm regretting it now.
Sorry if I sound harsh, but some of the complaints I've been hearing seem extremely entitled and poorly thought out. Fortunately in this forum, the complaints are legitimate, and thank you all for taking the time to read this. I hope my advice does help in some of the more rough or annoying gameplay incorporation in Crystal Kaizo.