USUM perplexes me on not wanting to "add" rather than "replace" content compared to previous 3rd-version games: Giratina and the Distortion World didn't do away with Cyrus or Team Galactic in their base or at Spear Pillar, for example. All you would need to do is insert the Ultra Recon Squad throughout Alola akin to Looker's appearances in Platinum (have them investigating Z-Crystals since they have similar energy to Necrozma/the Wormholes), and then perhaps follow-up one of the Lusamine battles with Nebby being taken by Necrozma (drawn to the battle by its evolution power and Lusamine tearing open Wormholes) to lead into the Ultra Necrozma battle.
If you insist on tying things together, Lusamine's reformation could go from a simple purging of Nihilego's toxins to a "dear god I caused this" reaction to Necrozma becoming (to her) a monstrosity (Dusk/Dawn) in tandem with her reaction to her kids having stood up to her lunacy. Not to say this would be better than how her SM self was written but at least it'd keep a flow between the new events instead of just kind of pivoting into new stuff and relegating the old climaxes to "oh and this happened" or haphazard decisions (Lusamine's insanity becomes "okay I had a plan" that still involves freezing a bunch of Pokemon?).
Hell, some of the USUM stuff makes less sense for USUM than Vanilla SM: Rainbow Rocket has to kidnap and brainwash Lusamine to work for them instead of hiring the equally-knowledgeable Faba who sold her out to begin with (which would beg the question why they didn't do the same with N from Unova instead of bringing the obvious-traitor-later Ghetsis onboard). Seeking out SM Lusamine would track because she was a Megalomaniac and much more capable battler for most of the story, and the concern could be down to her potentially joining up with them if she relapsed or simply being in danger to her health since she hadn't recovered from Nihilego yet.
This is why I consider USUM the weakest "third version" games, for a criticism I (to a significantly lesser extent) share with ORAS as remakes over Gen 3 and Emerald; for everything they add, they took away significant parts of the original such that even if they're superior to you, they have major gaps and reasons that prevent them from being OBJECTIVELY better or more up to date game experiences compared to their predecessor at respective release. USUM has a lot of cool battling and catching content, but the story, arguably the strongest suit of SM was definitively a worse one. It stings especially because it makes Gen 7 two halves of a really good Pokemon game rather than one strong whole. One could argue Gen 5 had a similar issue, but B2W2 was always presenting itself as a sequel, not a replacement/definitive edition, so it has less of a "need" to be the previous game but better on story.
And let's be real, if USUM was a thing nowadays it would have just been an expansion pack like Gen 8 and 9 have. The "3rd version" trend was always contentious with Pokemon, but USUM combined the biggest "not a strict improvement" feeling with being on the 3DS, a console that should be capable of DLC if the team was more forward thinking (to ensure the game had Assets able to be accessed and arranged for new maps and such rather than literally copy-pasting a copy into every map as was infamously rumored about Lillie's Model for example). Even if USUM are themselves fine games, in the context of Gen 7 and the Pokemon franchise they reflect some of the worst practices/incompetence by developer and publisher, and I'm willing to bet they contributed to the intensity (not necessarily validity/invalidity) of Gen 8 after them.
If you insist on tying things together, Lusamine's reformation could go from a simple purging of Nihilego's toxins to a "dear god I caused this" reaction to Necrozma becoming (to her) a monstrosity (Dusk/Dawn) in tandem with her reaction to her kids having stood up to her lunacy. Not to say this would be better than how her SM self was written but at least it'd keep a flow between the new events instead of just kind of pivoting into new stuff and relegating the old climaxes to "oh and this happened" or haphazard decisions (Lusamine's insanity becomes "okay I had a plan" that still involves freezing a bunch of Pokemon?).
Hell, some of the USUM stuff makes less sense for USUM than Vanilla SM: Rainbow Rocket has to kidnap and brainwash Lusamine to work for them instead of hiring the equally-knowledgeable Faba who sold her out to begin with (which would beg the question why they didn't do the same with N from Unova instead of bringing the obvious-traitor-later Ghetsis onboard). Seeking out SM Lusamine would track because she was a Megalomaniac and much more capable battler for most of the story, and the concern could be down to her potentially joining up with them if she relapsed or simply being in danger to her health since she hadn't recovered from Nihilego yet.
This is why I consider USUM the weakest "third version" games, for a criticism I (to a significantly lesser extent) share with ORAS as remakes over Gen 3 and Emerald; for everything they add, they took away significant parts of the original such that even if they're superior to you, they have major gaps and reasons that prevent them from being OBJECTIVELY better or more up to date game experiences compared to their predecessor at respective release. USUM has a lot of cool battling and catching content, but the story, arguably the strongest suit of SM was definitively a worse one. It stings especially because it makes Gen 7 two halves of a really good Pokemon game rather than one strong whole. One could argue Gen 5 had a similar issue, but B2W2 was always presenting itself as a sequel, not a replacement/definitive edition, so it has less of a "need" to be the previous game but better on story.
And let's be real, if USUM was a thing nowadays it would have just been an expansion pack like Gen 8 and 9 have. The "3rd version" trend was always contentious with Pokemon, but USUM combined the biggest "not a strict improvement" feeling with being on the 3DS, a console that should be capable of DLC if the team was more forward thinking (to ensure the game had Assets able to be accessed and arranged for new maps and such rather than literally copy-pasting a copy into every map as was infamously rumored about Lillie's Model for example). Even if USUM are themselves fine games, in the context of Gen 7 and the Pokemon franchise they reflect some of the worst practices/incompetence by developer and publisher, and I'm willing to bet they contributed to the intensity (not necessarily validity/invalidity) of Gen 8 after them.