Hey there! I didn't personally play this ROM hack so I can't tell you anything gameplay wise or glitch wise, but I did watch playthroughs of it on YouTube, including Fitz's. As such, I can comment on the way that the game is written. I know a lot of it would come from picking up the start of a plot someone else had written, and for what it's worth, I didn't notice any difference in writing style, which is a good thing! The writing blended seamlessly. That being said, the writing isn't perfect, and I think it's worthy of criticizing given how vastly it veers off course from the original FRLG story.
I'll start out with praising the plot twist with Deoxys vs. Mewtwo, which is of course a carry-over of the original ROM hacker's intention; I thought it was an interesting plot twist, and though it definitely had Black and White vibes to it, it still felt unique enough to stand on its own. I also liked how involved everyone was in this particular plot, which made the characters connect to you more. Daisy in particular is super praise-worthy in that she became a gym leader and she was still heavily involved, which made her really fleshed out as a character to me. The plot itself and its story structure works well, and I also like how the other protagonist was involved in the story, which reminded me of one of the few things I liked about the Sinnoh games.
The problem lies with how the information within this plot is conveyed. See, a lot of the dialogue of the characters is expository and absent of individual character, and while some exposition is necessary to ensure the player is on the same page as the plot, I think this ROM hack has a vast overabundance of it to the point that the exposition comes off less as getting the player up to speed and natural conversation flow between the characters and more fluff that conveys very little in many words. It got to the point that a conversation lasted so long that the person playing the ROM hack stated frustration with the cutscene; again, long cutscenes are all right, but only if the material is engaging enough to necessitate a cutscene and, unfortunately, it usually isn't in this case. Certainly this much exposition is nice if the plot is confusing, but the plot in this ROM hack is actually very simple, so the player has long since figured out what's going on within it by the time they've explained it like five times. As a result, the dialogue is also very repetitious, and that can turn people off of the story because they just want to get back to playing the game already.
A good example of this is in the plot twist with Mewtwo being the Pokémon Giovanni actually wants. You discover this in a subtle "Aha!" moment that's amazing for a player to experience, finding a journal that makes it sink in that this must be the thirteen-years-ago incident that Giovanni was talking about. This is a great way to convey this information, because it allows the player to piece together the story without insulting their intelligence. Unfortunately, the game then goes on to spout out a bunch of expository dialogue about what they just learned, and then to describe that in depth twice, before finally actually moving on to something new in the dialogue, turning what was originally a fun moment of discovery into "Yeah, yeah, I get it, can we move on already? Geez". This is only one of several examples of this happening throughout the plot. I think the most egregious, and thus the most insulting, example of this is when the player outright sees the Marowak die, which was a great scene by the way, only for them to be outright told later when they meet the ghost Marowak that it's the same Marowak through a dialogue box. This part is insulting because it really isn't hard for the player to deduce they're the same Marowak, and yet the script thinks the player is so incompetent at gathering this for themselves that it goes out of its way to waste the player's time in describing it, which can reduce the emotional impact of the scene.
You need to keep in mind your audience for these ROM hacks. You really don't need that much exposition for the player; much of those who even know about this ROM hack will be able to pick up the plot threads for themselves without the characters explaining them over and over again. If your concern is the characters even knowing about these plot threads, you could easily do an ellipsis which would imply that the protagonist is explaining everything that happened in the plot so far to them, and then have the characters react to that. They don't need to make such explanations overwrought.
Every line that you write should have some kind of purpose behind it, and you need to consider whether it's really necessary to include a line. That purpose doesn't need to be strictly plot related; it could be just conveying something about the character. Some of my favorite lines are in regard to Blue. I liked the little character plot thread going on with him in which it seems like he doesn't register how serious the situation is, but in reality he's more involved than Green is. Unfortunately, because the story focuses so much on this exposition, there's not enough time dedicated to this Blue and Green contrast, and the reason why this in particular stands out is because Green is noticeably less proactive in the plot than Blue is, something the game could've poked at (and even being a clever parody of HGSS, which has a similar issue of the other protagonist not being that involved in the plot even though they talk about things in the plot). In addition, I think it's a seriously missed opportunity not to have a double battle with Blue against any of the Team Rocket members, which could be especially significant in showing gameplay wise that Blue is actually being very helpful and competent despite Green's criticisms of him not taking the situation seriously.
My greatest concern character wise relates to Silver/Kamon. In HG/SS (and GSC), there was the heavy implication that Giovanni was his father. But what made HGSS and GSC so masterful is that it was never confirmed, and Silver/Kamon kept that realistic characterization of having his behavior informed by his relationship with Giovanni, but having it not explained outright in the script. I'm not saying that this should be a secret in this ROM hack by any means, but I think the overarching problem with the script in that everything is overwrought and overexplained hampers Silver/Kamon's plot thread the most. Him outright explaining that his mother died to some strangers he just met seems wildly inconsistent with how he hardly ever mentioned his familial situation in HGSS. I like the idea behind this, that he's trying to calm his father down and reason with him, but I think the execution gets in the way of this being impactful to those who play the ROM hack. Certainly it affected people as demonstrated in this thread, but I think it could've been better than it already was. Again, this is about letting the player connect the threads together. Giovanni could still talk about his revenge plan (once, mind you; he explained it multiple times in multiple different meetings, and I think that's a little much, explaining it once would have sufficed), mentioning his dead wife there, and then we find out through Giovanni's dialogue or simply in the way that he interacts with Silver/Kamon that he is his father. Through this, the player can piece together that Silver/Kamon was deeply affected by the same incident that Giovanni was, in a subtler way that stays more faithful to HGSS's intention. That realization that the player would have about this would make the player feel sorrier for him than if he explains it outright, and allows the player's imagination to run wilder.
Keep in mind, though, that I still adored this plot and I admire the effort that was put into writing it. It's one of my favorite plots of any ROM hack, and it's definitely well done, and it's very interesting to delve into! Really, the problem lies just in how overwrought it really is. Sometimes, less is more. I'm willing to go line by line and assess them individually to see what you could change if you need examples of improvement, but for now, I hope this post adequately conveys what I liked about the plot and what I think could use improvement. Now, if you don't feel like implementing these changes, especially since it would be a pretty big overhaul of the script, that's understandable; you can use this advice for future endeavors in ROM hacking. Or don't! It's fine either way.