The weird thing to me is they had a pretty reasonable set-up to use Penny's tech expertise at the stations: Stations 1 and 2 (or 2 and 3 if we make 1 "free"), have Penny need to hack in to get it online, when some aggressive Wild Pokemon attack and Nemona/Arven help you keep them off her back. The last station could be online already but have a mechanism she can't get into (EX: Arven using the Book to open the gate to Deep Area Zero) to fit Penny's Battle in. Then Station 4 is opened by the Professor and things proceed as we see in the final game. This mostly requires a few text box changes since you can just have the "hacking" off-screen while you're battling the Wild Pokemon.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.
One thing I'll mention initially, one of the Diamond/Pearl Manga adaptions depicts the Lake Trio as asleep during the Lake Valor sequence (the characters fighting back awakens Azelf briefly in response to their willpower), and they're drawn as being sort of painfully-shocked awake at the Galactic Building. I had always assumed the Legendaries were sleeping and captured/secured before they were awake enough to fight back (especially since the Lake Trio are in the "Minor" Legendary category that's usually depicted as catchable). Cyrus's plan is depicted as effectively ruined when the Red Chain is broken, so it's clear this object, which required an operation to catch 3 other Legendary Pokemon with heavy tech and a base they have lost now, is the only reason he could get Dialga/Palkia to even attempt what he was after. The Lake Guardians don't have a physical power over them, they just pacify them on a spiritual/emotional level to not say "screw the Universe, where's the reset button?" and then leave.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.
I also think it's important to note that in this Avatar theory, this particular idea is a retcon in the games without total consistency in the Anime Arceus, namely the fact that M12 features it fighting the Creation Dragon trio, which wouldn't make sense if thy were all extensions of the same will. I kind get the sense the Sinnoh Legends aren't really Avatars or Puppets the same way the God Llama is, at most they strike me as entities Arceus creates to give order to these forces but doesn't have direct control of. The HGSS event already confirms they can just be created on a whim by Arceus so it's not like they so-absolutely embody the concepts as to be the sole existence even before Multiverse shenanigans happened.
All this acknowledging it's retconning, because I think it's also the case that in 2005-6 (Development and release), Pokemon simply didn't emphasize story enough to consider what kind of scale a monster like Time & Space Deities should actually work on, something you do see in other media like how DC constantly has to figure out how the hell The Flash operates in a given iteration.
Personally, the Sinnoh Legend stuff never bothered me a great deal because I don't think the games depict them getting as far as proving the feats they're trying besides Giratina and the Distortion World existing, and a lot of their other powers/feats are brought up in lore books but never seen through outright in the Games. My interpretation had always been that the Sinnoh Legends aren't actually Capital-G God Pokemon equivalents, rather they're extremely powerful and revered as such by Sinnoh of old. In Gen 5 the equivalent would be the "Original" Tao Dragon, Gen 6 presents Mega Rayquaza as such in Hoenn, and I'd argue such an idea could be applied to Ho-oh and Lugia in Johto retroactively. As for the difference in feats/scales they recount, just consider how wild some Mythologies in the real world get compared to each other.
- Christianity/Judaism: "God speaks through a burning bush and unleashes 10 Physical Plagues on Egypt"
- Greece: "Kronos devours his kids and a rock only to be made to spit them out and be overthrown. Zeus eats another Goddess only to get a literal splitting headache which his Daughter Athena pops out of full grown in battle armor"
- Norse Mythology: "Every object and concept in existence swears not to hurt Baldur, making him basically invincible. Also Gleipnir is made out of 6 ideas that don't exist any more because they were used to make it."