Costume/skin are things like Hero taking on the form of various heroes. Pallet swaps are things like Lucina taking on the colours of various Awakening characters. One changes the full model; the other just changes the colours.
In BBTAG, every character's 9th colour swap has them take on the colours of a BlazBlue character, the 10th has them take the colours of a Persona character, 11th for Under Night, 12th for RWBY. It's probable that Arcana Heart, Senran Kagura, and Akatsuki Blitzkampf will have ones added as DLC. Meanwhile, in Chronophantasma, every character has a BlazBlue, Guilty Gear, and Persona pallet.
I'm suggesting Smash could just port over the BBTAG pallets for bonus anime fighter referencing points, not doing full model swaps, as that wouldn't work for a lot of the characters as you pointed out. It would be really funny to see Heart wield aramasa though.