I'm not entirely convinced that she IS UB-001 to be honest. My guess is that UB-001 is the moving thing inside her bag in her first trailer. She probably smuggled it from totally-somehow-related-to-her Lusamine and the Aether Foundation and it started to mimic her form.
My guess is that either Lillie is UB-01, or it's going to be a case like in Pokemon Heroes (anyone remember that?) where Latias shapeshifts into that girl.
Now that you mention it it's possible that it's not literally Lillie it could be the creature imitating her form. It may even be a case like ash's greninja where they bonded. It's most likely connected to team aether too.
The connection is pretty much undeniable though. The resemblance is almost blatant especially when when you see the legs that ub-01 has
Maybe the Aether Foundation had been studying UB-01 in captivity where it was befriended by a younger Lusamine mimicing her appearance. Some incident occured and it escaped the AF while still retaining the appearance of young Lusamine eventually being taken in and protected from the AF in secret by prof Kukui for some years.
While putting on the friendly front of caring for Pokemon, the Aether Foundation may have been experimenting on UB's to turn them into some kind of brain washed special forces unit. Hence UB/Lillie's dislike of Pokemon battles.
Edit: Another random thought for the anime adaption of SM. Satoshi lands at Alola quickly hearing rumors about legendary Ultra Beasts and becomes determined to catch one. Searching for them across Alola with Lillie not knowing the whole time she was actually one of the UBs he was looking for.
Here's something weird I noticed somewhere else, sparked by the mention of the portal.
Lusmine says that she welcomes creatures from different lands "even distant ones like alola region" so that would imply they're NOT from the alola region, so where the hell are they from?
Then we see all these weird experiments, and they seem intimately connected to a being that comes out of a portal and looks like it could be a human.....
Is it possible they're all some kind of alien or ultra beast?
Eh, probably not I just found that theory kind of fun
As fun and interesting these Lillie, Lusamine Ultra Beast theories are I would have preferred they kept it secret. The game isn't even out yet and assuming it really is true they have already spoiled a major plot point of the game.
Like how the trailer for Terminator Salvation showed off that Marcus was a cyborg before the film even hit cinemas.
Well, the game is out, and turns out it's almost a coincidence.
Actually, way I had it explained to me is:
Rather than Nihilego looking like Lillie, it's Lillie looking like Nihilego, as Lusamine dressed Lillie up in a controlling, specific way to make her resemble the object of her obession.
Rather than Nihilego looking like Lillie, it's Lillie looking like Nihilego, as Lusamine dressed Lillie up in a controlling, specific way to make her resemble the object of her obession.
Evidence suggests that Lusamine hadnt seen a Nihilego until she summoned one in game.
Lusamine really wasn't surprised at all when Nihilego first showed up in the game, for what it's worth. Considering how the game hints that Lusamine was really nice before her husband disappeared and she became obsessed with the UB's, it'd make sense that she was affected by Nihilego for a while.