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?).
		
		
	 
Honestly I was fine with the changes they did to Lusamine in USUM (up until the resolution point). In SM, when it was JUST Lusamine, it makes sense she would just become obsessive over Nihilego and her plan would just be living with them. USUM throws in a new plot element, the Ultra Recon Squad, who came to the Aether Foundation with their problem concerning an Ultra Beast, Necrozma, having stolen the light from their world and is likely going to do the same to the Pokemon World. This addition changes Lusamine's focus to Necrozma, seeing it as a creature in suffering, and not only will she be helping it but as a bonus she'll be saving multiple worlds (but note that the "saving the world" part is just a bonus to Lusamine, she still only cares about the Ultra Beasts)!
So for Lusamine I would pretty much keep everything with in her USUM as is, up until reaching the Alter where her and Guzma are kicked out of Ultra Space (but before Nebby evolves to Solgaleo/Lunala). Instead of having Lusamine injured and terrified, she gets up and is furious that Necrozma would not accept her love. THIS is where they can then move the Lillie confrontation; not off screen, but rather have Lusamine be "alright" but crazy so that Lillie can tell her what a horrible mother she is (of course Necrozma can't accept her love, what love does she have where she doesn't have any for her own children?). This is where you can throw in an extra Lusamine battle (or move the Lusamine battle to here), but eitherway Necrozma soon appears. Still angry as Lusamine, it attacks her, but Lillie jumps in the way of the attack. Seeing Lillie in danger, Lusamine snaps out of her anger and tries shielding Lillie. But before the attack lands, both are teleported away behind everyone else: in their place absorbing the attack is Cosmoem-Nebby. This is when Lillie and the player both play the flutes and Nebby evolves to Solgaleo/Lunala and we have the epic battle between it and Necrozma... only for it to than get absorbed and flees to Ultra Megaloplois. And from here the player is lent the URS's Legendary while Lillie stays behind, feeling like her and Lusamine can finally have a heart-to-heart.
It there's any problem with the story pacing, it's the Ultra Recon Squad. Their added scenes don't really give them that much development time (not to mention the battles with them are disappointing as they only use one Pokemon). They needed more time, better battles, and of course Ultra Megalopolis made into an actual city instead of glorified hallway.
	
		
	
	
		
		
			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.
		
		
	 
I know 
R_N already pointed out some stuff, but just wanted to also mention a better way to use Lusamine in the Rainbow Rocket arc that would have left her in a similar situation as in the end of SM (thus keeping the story point of Lillie needing to go with a sick Lusamine to Kanto).
Instead of an invisible Ultra Beast having put Lusamine to sleep, instead Giovanni could have summoned a Nihilego to intoxicate Lusamine which turns her back into her SM personality. Lillie tried to get through to her but she brushes her aside, saying she only needs the Nihilego and fuses with it to become the Mother Beast. Player battles and defeats her, and while stunned Wicke tosses a Beast Ball from a higher platform she's observing from to capture the Nihilego and forcing it to unfuse with Lusamine who falls unconscious. From there you battle Giovanni, defeat him, clear out Rainbow Rocket, and after some time we end on a scene similar to that of SM with Lillie's departure to Kanto.
	
		
	
	
		
		
			-The thing that drives me nuts the most, though (which maybe we've covered this in this or another thread before and I just perpetually forget if anyone has had a counterpoint) is that at the climax the Ultra Recon squad already has a Solgaleo/Lunala, making all of the business with Nebby seem pointless. This always felt like a big plothole to me.
		
		
	 
I wasn't bothered by that as much. Up until the Alter, you really weren't working with the Ultra Recon Squad, at most you were an interesting subject to observe and at worst you were an obstacle. Their Legendary is the ONLY way for them to get back home, they're not going to give it to just anyone unless they absolutely needed to. After Necrozma fuses with Nebby and its clear only the player and their Pokemon has the strength to go up against it do they acquiesce and give us access to their Legendary to ride to Ultra Megalopolis.
	
		
	
	
		
		
			It's something that's really easy to overlook in the thick of things and I find that when it first comes up people's reactions are "I must have missed a full conversation" and not literally one line
	
	
		
		
			"The president will not awaken for some time. I have used the power of that Ultra Beast to make her sleep... And when she awakens next, she will be a loyal servant to my will!"
		 
		
	 
like even if it was just Nihilego (which would be weird because this is not how the toxin works) or hell Pheromosa (still doesn't put to sleep but does have a control aspect) like idk bro maybe you could show it to us seems pretty thematically important to Lusamine's character. Hell Nihilego wouldn't be 
that out of place on your team
		
 
Huh, weird. I wonder what the Japanese line was, because this is VERY strange. I'm wondering if maybe he said something like "
I have used the power of those Ultra Beasts" or just "
I have used the energy from the Ultra Beasts", which makes a little bit more sense as he's just saying he used the Ultra Beasts energy instead of a specific Ultra Beast that's apparently in the room with them.
	
		
	
	
		
		
			I seriously wonder if one of the big execs in Japan didn't like the portrayal of an abusive parent in their games and made the writers minimize that element in the sequel.
		
		
	 
Maybe, they also notably dialed down the "subtle sexualized" tones the original game had at points:
- During the Water Trial, instead of Lana imagining its a hunky male swimmer that needs help, she just says it sounds like a Pokemon needs help.
- During the Grass Trial, instead of the minigame where you're mashing the ingredients together into a goop to a view of Mallow's crotch, she just puts it all in a boiling pot.
- Instead of Lillie going with you to Exeggutor Island to fetch the other flute, only the player is allowed to go (and post game the cave scene between Lillie & the player in SM is replaced with a similar joke scene but it's with the boat captain).
I can see parents complaining about the mature content the game had "hidden" in it and so in USUM decided to dial it back.