There is never going to be a plot worse than Sinnoh's (DPPt/Arceus movie/Giratina movie) in Pokemon.
Any butchery made to human characters in the series cannot overshadow the extreme butchery done in the execution of gods who were meant to define all of Pokemon lore and the universe(s) they shaped; Pokemon who were meant to be at the very pinnacle in terms of power-level. These Pokemon make digging into the lore feel meaningless at times because the games / movies expressed ridiculous amounts of plot armor against the entire lake trio, creation trio, and Arceus, in a manner either not as present or not as severe as in any other generation's media. Every time I bring this up people are like "isn't every Pokemon story like this?" The answer is no. No other generation gets this ludicrous amount of plot-induced stupidity.
For example, in Gen 6's case, Team Flare was able to get a hold of Xerneas/Yveltal by sneaking them into their base while they were sleep. Lysandre tried to get their life energy drained but they eventually woke up on their own, broke free from the weapon, took back their life energy, and showed Lysandre who was boss. - okay that's actually reasonable.
In Gen 3, Archie and Maxie raided building after building ran by human communities everywhere in order to gather the resources needed to access the legendary box art. They've obtained the resources and then reached out to Kyogre/Groudon, who then proceeded to break free, go out of control, and show Archie and Maxie who's boss - this is also reasonable.
A similar thing happened with BW as with Gen 3 except a legendary Pokemon willingly sided with the main antagonist of the game. N did not attempt to force Reshiram/Zekrom under his control.
In B2W2, Kyurem was captured and used. Okay sure, but conceptually, Kyurem is a soulless empty shell of a Pokemon deprived of any motivation to do anything but eat and sleep. It needs help. It needs to see the light in truth or ideals in order to gain the motivation to do something. This is a reasonable explanation for how Kyurem managed to get captured and used by Team Plasma in B2W2. Additionally, Kyurem was designed to be nowhere near the level of deities that control time, space, or all of existence. Kyurem is just able to freeze the world with ice. Not shape up entire universes or define the entire nature of Pokemon as we know it.
In Gen 7 the only legendaries captured by human antagonists were baby Pokemon. Aside from that, Necrozma managed to get control of Solgaleo/Lunala but Necrozma was designed to be a force above them anyway.
Gens 1 and 2 didn't really use their legendaries much in the plot aside from making them glorified trophies. Gen 9 turned their legendaries into glorified regular Pokemon with little substance.
Gen 8 simply had legendary Pokemon do their jobs. Nothing more.
Team Galactic were actively messing with Pokemon gods, whether it was Uxie, Azelf, Mesprit, Palkia, or Dialga. Almost all of them canonically had the power to see what Galactic were doing well ahead of time and intervene. All 5 of these Pokemon had every capability possible to avoid the situations they were stuck in. Uxie could dismantle Team Galactic just by opening its eyes and even know what Galactic were doing before the team even reached it. Azelf can manipulate or remove their will, even control them for its own desires. Mesprit could play around with their emotions. All 3 could've done the exact same thing they usually do when you see them; just randomly disappear into somewhere far away. They could have done that to escape as the very last resort if that was ever needed, which it wasn't. Dialga is the embodiment of time. The literal nanosecond it appeared out of its portal it could have ended up in 50 different points of time simultaneously to stop Team Galactic from ever getting a hold of the Red Chain. Palkia could've just erased Cyrus within that same timeframe. Giratina was just shoehorned into the same climax as DP to save the day, with no real explanation until 13 years
later with Legends Arceus. Giratina's lore barely even got fleshed out in Platinum. All we did was "enter its home". It's honestly less so than Xerneas/Yveltal (who got more than you'd probably expect but a lot of information is given by random NPCs in houses) but people disagree because "Distortion World looks cool". Aside from this, in Giratina's movie, Giratina got captured by an antagonist while alive, active, and awake, and nearly died to a machine, very much unlike the case with Xerneas and Yveltal, despite representing a concept beyond Xerneas and Yveltal. Arceus was... well, https://www.smogon.com/forums/threads/unpopular-opinions.3530232/page-492#post-9432356
. Unlike Kyogre, Groudon, Xerneas, Yveltal, they were not able to defend themselves from abuse/being misused/mishandled by antagonists. Unlike Reshiram/Zekrom, they were not willingly siding with the antagonist. Unlike Cosmog, they weren't babies designed to be among the weakest of Pokemon, and unlike Kyurem, all of their power-levels were above and beyond for the series. Gen 4 truly did more harm than good to Pokemon lore thanks to their stories. It's shown by how for example, people believe Arceus to not be the defining Pokemon in series lore due to how it almost died to a meteor and got defeated by silver water.
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.