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I enjoyed the concept of the Ultra Recon Squad, but their home dimension was really a disappointment. It would have been nice to explore, even if to collect rare items and battle trainers. It could have been the "black tower" of USUM. I think Lusamine should have been softened personality wise...

Well, clearly there are two different stories between USUM and SM, so it's safe to say yes.

You run into looker once you leave Diglett's Cave (I think that's the location) on Akala island, be blabs about the birds and bees, and mentions an odd stone he found at Olivia's Shop, and then proceeds to give you a fire stone. If the fire stone is the odd stone, then well Looker hasn't been...

I think that "odd stone" that Looker got at Olivia's shop was the Audinite he had when he "fell" into Hoenn's postgame, thus probably the strongest link between Gen 6 and 7 I've seen besides the souvenir.

So, does Lillie go to Kanto in USUM? I don't want to know what happens in terms of the ending, just want to know if the Lillie Kanto thing changes.

I wouldn't read too much into things. No explanation for Anabel, but for Looker when he showed up in the post-game of ORAS, I think GF wiped his memories to simply to leave details of how he landed in Hoenn to be completely ambiguous.