My main problem with the changes made was that they still kept a lot of the game's previous build up only to then not deliver the pay off that SM delivered.
A thing to remember here is that all the characters are the same, Lusamine here is just as crazy as Lusamine from SM except instead of transfixed on Nihilego she's going to stop Necrozma. Of course, the problem with doing that is the player never sees how crazy or cruel Lusamine truly is, you just have to take Lillie's and Gladion's word on it. Yes, Lusamine does tell them they're no longer her children and doesn't care that Nebby may die... but it's portrayed she's doing it for the greater good. She even says that, despite the way they behaved, her actions will also save Lillie and Gladion along with everyone else. She doesn't call Lillie "ugly", she doesn't say she couldn't care less if Nebby dies or if the Pokemon World is destroyed by Ultra Beasts, nor her shruging off Lillie telling her she's terrible. You're still suppose to root against her, but her actions only make her seem like a well-intention, if prideful and selfish, extremist only doing what she believes would save the world at cost of her family's relation. We also don't get to see Lillie talk down her mother (happens off screen) and, while still makes sense it happens and why Lusamine would be interested, the significance of Nihilego's appearance in the Aether Paradise is lessened (no longer is it the UB that Lusamine wants to be with, now it was just a random UB to prove their experiments were working). Also, while I said they're the same characters, it does feel Lusamine's character is being pulled two ways as wanting to stop Necrozma somehow mitigated/cured her insanity somehow? Like, okay, I could see her re-evaluating her outlook on things upon failing to stop Necrozma (and thus not poisoned by Nihilego), but it happens before when she's being all righteous when going into the Ultra Wormhole.
AND then there's Gladion and Silvally not getting their pay off, instead of battling back Nihilego from entering our world he now just begs Lusamine to take him with her instead of Guzma and is told no. That's it, that's where Gladion's character development and hardships lead him. Now, I do like USUM's ending for him better, him setting off to Kanto instead of Lusamine and Lillie, but I don't like what was done to get him there.
Lillie also got his hard. Not being allowed to go to Exeggutor Island, not seeing her talk down her mother, and though she's a trainer now in the Rainbow Rocket story it's just a Clefairy, goes back to a healing role, and is even held hostage and has to be saved. This even effects the credits as SM's credits were pictures of what happened to characters being sent to Lillie by Hau (plus the first picture Rotom Dex took of your trio and an Island Challenge Amulet (though Lillie has a non-viewable version of it on the desk of her loft in the lab)).
I was actually kind of hoping we'd have a side quest where we followed Lillie on her Island Challenge (giving us a story reason why to revisit all the islands aside our own curiosity).
Also, I just met Looker and Anabel on Poni Island, looks like they removed their side quest so there goes that character development. You couldn't work them in somehow, like maybe make it impossible to catch Ultra Beasts outside of Ultra Space. You first help Looker and Anabel push back the Ultra Beasts but then have to go into Ultra Space to capture/defeat them to fully close the Ultra Wormhole they came from.