The only people actually missing are the Elite Four, who were claiming to be hosting the Prom and don't seem to be there! The actual Indigo Gym Leaders were simply not invited because Team Rocket...really did not want to face all of them at once, and their attendance was not mentioned on the invitation. Characters who have been to previous proms hosted by Claire and full-up on Gym Leaders are free to find that kind of weird!
The Aurora Gym Leaders will have received a standard invitation by Spearow! Team Rocket doesn't seem to be terribly worried about the Aurora League just yet, as they aren't as established and there are only two members, but them being there will be seen as a plus since as champions they probably have some sweet rare Pokemon. In the chaos they will probably be targeted the same as any other trainer unless they start shouting about being leaders! In that case, they might get a few more Rockets trying to take them down, but it's up to you how to play it out!
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The Aurora Gym Leaders will have received a standard invitation by Spearow! Team Rocket doesn't seem to be terribly worried about the Aurora League just yet, as they aren't as established and there are only two members, but them being there will be seen as a plus since as champions they probably have some sweet rare Pokemon. In the chaos they will probably be targeted the same as any other trainer unless they start shouting about being leaders! In that case, they might get a few more Rockets trying to take them down, but it's up to you how to play it out!