I'm also a 2013 player, but I was 8 and don't remember much. I went through all 4 regions and bred a couple 6x31s after in 2020, and I just kinda plowed through all the gym leaders and elite fours. I'm also dogshit at pokemon, I don't play competitive.
Shedinja's nerf: When it happened, I saw most of the community's active players all agreeing with it, so... If you want to rebattle the elite four, then make a team of good pokemon and have a good strategy instead of cheesing it with a shedinja. That's like cheesing a boss in a game; the devs didn't intend it so they would obviously remove it.
State of PokeMMO: Like before, the game isn't hard. Anybody the age of 10 and above shouldn't find any difficulty, it's just that they bumped it from very easy mode to slightly above normal mode. The shiny rate is buffed because it's an MMO, and there's an economy. It reallly shouldn't be that hard for you to understand, it's not bullshit.
By the way, as far as I know there's no guarantee that the shiny rate wasn't 1/30000 in 2013.
Here's a comment by Kyu that says the shiny rate is 1/30000 in early 2018. This is the forum post that says what the shiny rate is. Kyu also says that it hasn't been changed in a while, so that means it could've been more or less before.
PvE balacing: They're not hard, the balancing just makes it so an average player can't beat them without levelling up and deciding on a good team. In other words, the balancing changes the regular pokemon story (easy games that young children can beat without much difficulty) to a game that people who grew older can enjoy. A lot of the active players aren't young children, so it makes a lot of sense to make the game more difficult. Basically, instead of beating every gym underlevelled with no strategy, level up your pokemon more and think about how you can win, and you will.
Buff charms/items: No, they're not useless. See, if these items didn't do anything they would be useless. But they do things. So they're not useless. Not hard to understand. I use shiny charms for farming shinies, I use lucky eggs for farming exp on new pokemon. I used to farm lucky eggs in the safari when I played more, I love how rare it is. See, most of the community just assumes that they'll never get one, when it's actually not that hard. I just watch a movie or listen to a podcast while I farm lucky eggs, and then whenever I get them I sell them for 200k. I used to get about 2 or 3 each day farming for a couple hours, it's not boring because my attention is on the movie/video/podcast/music.
Suggestion for PokeMMO: Shedinja was nerfed for a good reason, and like expected the active players of the community agreed with it. The shiny rate was changed to 1/30000 under the assumption that it would work well with the economy system of an MMO, and wouldn't you believe it; it did. It's been 1/30000 for years, there's absolutely zero reason to change it now, it still works well and it probably will until PokeMMO is ended. Pay to win? What? There's nothing you can buy that makes the game easy for you. You can buy move ocarinas, which are a great feature and are definitely not pay to win. You can sell the cosmetics that cost real money for in game money, but that won't make the game easier. Donator status is a reward from the developers for people who want to support their FREE game. By the way, 1/30000 to 1/27000 SOUNDS like a lot, but all you have to do is stop looking at 1/30000 and only look at the rate 1/27000. 1/1000 is considered extremely hard and most people wouldn't even think about trying, but 1/27000 is a different story. The game is obviously not pay to win. Why would they nerf gyms for newer players? They're not hard, just don't go in with your underlevelled starter and 2 underlevelled pokemon that you thought looked cool, and you'll win. The pokemon move pools are fine, I've never thought about them once and you're literally the first person I've ever seen complain about a move pool. I don't know what destiny bonds do, but this breeding system is fine and it'll hold up until the game ends. EV training takes like 15 minutes if you're slow, stop complaining about EV training. It's not like the devs are ravaging the game and throwing in micro transactions and pay to win, the only thing that could possibly be considered pay to win is the donator status, which is pretty obviously not for the story. You don't buy that to win, you buy that a long time after you've won. They added that years ago, "stop making everything pay to win" doesn't make sense.