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Deluxe versions/sequels should never be on a different hardware from the originals. That said, this is what I'd do.
>Gen 7 will be on the 3ds. SM's plot is reworked to make the UBs more prominent, trials are far more fleshed out, including Ryuki and Kahili trials from the get go
>Skippable cutscenes
>Guzma, Lusamine, Victory Road Hau will all have 6 pokemon. Hau is the first champion challenge instead of Kukui like in USUM
>Lillie gradually becomes a trainer alongside you.
>Steven, Lance, Alder, Diantha, and AZ are all part of the Battle Tree.
>Red's team is at the same level as it was in HeartGold SoulSilver, along with a starter that mega evolves. Said starter is the one that has a type advantage over your chosen starter.
>No Rotomdex gps.
>An improved PSS and no Festival plaza
>USUM are still dual versions, but instead of sequels they play up the alternate reality concept.
>Character roles are flipped. Lillie, Gladion and Lusamine have a good relationship
>Guzma is a trial captain
>Hau is a more serious and prideful rival, who picks the starter stronger than yours.
>Hau makes it to the league before you.
>Ultra Recon and Necrozma are the villains in place of Aether and Skull
>The Battle Agency is expanded, with several facilities from the Frontier, along with new Frontier Brains esque leaders, including an older Benga.
>There are 2 new islands in the game, and new routes and towns.
>Battle Tree now includes Elite Four members from every Generation up to that point
>Rainbow Rocket is expanded. Steven, Red, Colress, Cynthia, Guzma and AZ all help against the respective villain character.
>All the villain characters carry 6 pokemon
>The Necrozma battle will have 3 phases, where in which you won't be able to heal or save. The first is its base state, the second the box Legend fusion, then the Ultra Necrozma form. First state is at level 45, then level 50, then level 60.
Also: Chicken keeps her original outfit.