>>34123942BW2 set a precedent for dual "third versions", so it was reasonable to suppose they would do they same again. Ultra was a central concept in SM, so it's also reasonable to guess that would be the prefixes. Again, nothing remarkable.
RR was a mispelling of TR. If you look at the way he phrased it, "more returning baddies, specially RR" it doesn't make sense if you think RR meant Rainbow rocket. USUM was when RR debuted, so they couldn't be "returning baddies". He definitely meant TR(team rocket). He probably liked Colress(who was a baddie in BW2) in SM and wanted more of that.
Except lusamine is still a "villain", the story is pretty much unchanged, she's still a psycho unt that mistreats her children. "Lusamine taking a chill pill" my ass
Zeraora was simply omited from SM code to prevent it leaking before GF was confortable with it.