Also, why aren't Penny/Nemona used better in the endgame? Penny's story is about tech being used to isolate yourself, Nemona's character is about never knowing when to dial it back from 11. And yet neither of them has anything to say about a Professor who isolates themself from their family in order to over-focus on their work.
Aside parallels you can connect with the Professor, I do agree that Penny and Nemona feel tacked on for the final story and the only reason they're included was an excuse to not go right into the final story after defeating completing Path of Legends without completing the other two storylines.
Penny was brought along because they needed a tech expert. So, what is her contribution to the final story? Turning the lights on in the Area Zero Gate. That's it. No other time is her tech expertise needed. Don't get me wrong, I like her interaction with the crew, being sassy (though realizing when she went too far) and using common sense. However that's not why she was brought along, and the most baffling thing is that they could have given her further tech things to go. On our way down Area Zero we had to re-activate the Research Stations. Now, just entering them automatically gives the Professor access to them, but they could have at least had Penny be the one to turn it on (and maybe require the player, Arven, and Nemona to go check on something while she does her techy stuff) and contact the Professor. Yes, gameplay wise it doesn't change anything, but would have given Penny more of a reason to be there in-story.
Nemona was brought just to be extra muscle which she does so, always ready to jump into battle. However, I do feel the game missed an opportunity to add some depth to her character by making her realize her battling obsession (especially with finding another trainer as strong as she is) inadvertently prevented her from using her Champion position to actually help people in need. Because Nemona isn't just any strong trainer, she is a CHAMPION. A trainer which, in theory, if someone was having a problem that could be solved by battling they could go to her and ask her for help. On top of that, she's also the Student Council President, so once again any problems a student is having they in theory could approach her for help. While travelling through Area Zero they could have had Arven and Penny quickly tell the others about their struggle (Arven with healing Mabostiff and Penny with Team Star) and how the player helped them. And they could have then made Nemona realize how neglected of her positions she's been. Here are two students (or more if you count all of Team Star) who needed help from a strong trainer... but Nemona's obsession made it so they didn't even want to approach her, or worse she may not have even helped if they did. And considering how Nemona treated both Arven and the Team Star grunts at the beginning of the game (and now learning Arven was trying to get help for Mabostiff and all of Team Star bully victims), if I was Nemona I'd feel a little bit guilty. But no, all throughout Area Zero she is all cheery and battle-focused; even after Arven watches the robot version of his dead parent teleport themselves away, a pretty soul-crushing moment for him, does she try switching topic to how cool your 'Raidon looked while battling (Nemona, too soon...).
I also feel like the endgame story needs a refocus, but coming from the other direction. I end up thinking of the Professor and the Professor-AI as separate characters, so the issues with over-focusing on their work aren't the fault of the final boss. As far as the interaction with the AI itself goes, we the player are just there to crush their dreams with the harshness of reality. A role that I can't help feel is out of place for the kind of media a mainline pokemon game is. It feels like the AI's story is desperately missing either a "here's how your passion can fit in" (show the AI prof, who was presumably not been keeping up with every development in the rest of the world, tyrunt/porygon?) moment or a "don't feel bound by the path your parent/creator set for you" moment.
Kind of confused what you're getting at here.
In term of personality, the Professor and AI are different characters. The Professor was obsessive to the point of madness, while the AI realized how wrong the Professor was and wanted to stop their plans. Thus, the player didn't crush the AI's dream, the player helped the AI achieve its goal of stopping what the Professor started since it was unable to. When you're battling the AI you're not battling the AI who called you down there, you're battling what is essentially the Professor's ghost in a computer program form. And even when it was all over, the AI still achieved what it wanted to do by teleporting itself into the past/future (yes, it did so because it "inherited" the curiosity of the past/future from the Professor, but the Professor wanted to bring the past/future to the present. The AI set its own path based on the Professor's interest, but was still its own path). The only dream that was crushed was the original Professor's, and they're dead; even if their ecological nightmare dream did come true they wouldn't be there to witness it; in a way they crushed their own dream by consequence of playing god to achieve their crazy & dangerous idea.
At the end of the day, the Gen 4 legendaries and mythicals were intended to be Pokemon far beyond every other box art in terms of power and relevance in the lore, but were simultaneously treated as the most pathetic ones. This severely lessened the value of Pokemon lore and theories in general imo and it's shameful.
Which is probably why, for Arceus at least, they decided to go the "avatar" angle. It's not ACTUALLY god you're catching, but rather its the physical puppet god created to interact with the world cause it's too metaphysical to do so.
Thus, I wouldn't be surprised if all the other Sinnoh Legendaries connected to Arcues were too just "avatars" of what they represented. Dialga and Palkia aren't literally the embodiment of time and space, rather like the Arceus Avatar they're physical puppets with the power of time and space so it can have them manipulate those forces on a "miniscule" scale. Heck, maybe that is why Dialga and Palkia exist; why would Arceus need them anyway if its god of everything? Well because the Arceus Avatar doesn't have enough room to fit in the power of "time" and "space", so made a Time Avatar and Space Avatar as a compromise. Giratina exists as a Counterbalance Avatar, encompassing anti-matter (as well as anti-time and anti-space) so reality doesn't break down while the other Avatars bend reality (unfortunately this made Giratina a tad bit violent so Arceus had to shove it into the Distortion World where it can still do it's "job" but there's no concern of hurting anyone). As for the Lake Guardians, they were probably made not to create their spiritual traits but as yet as more tools for Arceus Avatar. Arceus Avatar doesn't look to have any control over sentient life, thus needs the Lake Guardians to manipulate them.
"Okay, so they're all "Avatars" of what they represent, so what? They're still incredibly powerful Pokemon who could have easily defended themselves from Team Galactic"
Could be Team Galactic, or rather Cyrus, pulled some loopholes in order to get around getting him & his team obliterated by them. Going after Dialga & Palkia directly was a no-go, they would be destroyed without something to control them. Hence they needed to go after the Lake Guardians to make the Red Chain. So, why didn't the Lake Guardians fight back? Cause they were inactive. Just like Dialga and Palkia as long as they were in their dimension (note the Lake Guardians dimension is the normal Pokemon World). Dialga, Palkia, and the Lake Guardians are loyal to Arceus (Avatar), so unless being actively used by it they're inactive. Giratina is the only exception as it has revolted against Arceus' control, but it's stuck in the Distortion World (at least until, in Platinum version, the timespace distortion caused by Dialga & Palkia allowed it to crossover though only to attack the one who was messing with the balance of the world: Cyrus). Galactic captured them while they were inactive, them only reactivating after what was needed to make the Red Chain was extracted from them. And so, with the Red Chain, Team Galactic could now summon the Dialge or/and Palkia and take control of them, forcing them to use the power they only use at Arceus' command to create a new universe (until its stopped).
So looking at them in that light it makes sense why Team Galactic was able to get the upperhand... of course this is a retcon as at the time they were very likely meant to be taken as deities.
mega-garchomp is way worse than mega-audino
Well if you go by comparing them to their base forms, yeah.
M-Garchomp losing 10 points in Speed is a pretty notable nerf, and one likely done on purpose. If they kept its Speed at 102 and instead only increased its Attack to 160 it would it would still be super busted. They couldn't add more to its HP, adding more to its SpA would just make it into a mixed attacker, adding more to its defenses would make it too bulky, and adding more to its Speed would just make the problem even worse. So, the only option they really had was decreasing its Speed, which turned out making it worse than base Garchomp who had no problem hitting hard. Also losing getting Evasion in Sandstorm for getting just more power (aka something it doesn't really need) was just an extra nail in the coffin.
Meanwhile M-Audino was an improvement to base Audino all around. No stat decreases, made into a wall by just pumping up its defense stats, and given a better Typing which helps soak damage from the most damaging Types. Sure its disappointing it lost Regenerator, but then again M-Audino is clearly meant to be a Double Battle partner and so makes sense using Healer instead.