>>57952274
That is a very nice lore, I like how you put it together. Deoxys and Team Flare sound like they go together well. Also, I don't think the idea is dumb. It is not as if people can't move around regions in Pokémon. After they get beaten, I could see remnants of enemy teams moving on, maybe in a fractured state. I recall sometimes Teams from older games show up as new teams, usually with some dialogue like "I used to be part of Team Rocket!"
>there's no team to take down, or real villains to overcome, outside the two's own personal demons really
Honestly, the League Challenge is more than enough. Getting all 8 badges is one for one with personal growth.
Funny enough, Neige was an experiment by Team Flare as well. I don't know the full details but I know the general flow was
>Neige was made from a bath of many Ralts
>She was considered a failure and was likely to be dumped
>Her first trainer, White, found her inside a burning Tem Flare truck and brought her along
>White had to abandon her, and she found Quartz a few years later
>>57950389
>does that still apply in the sort of alter ego state you mentioned?
Yeah, the way Quartz found out about Hiver was that he realized a bit late that Spes wasn't really Spes, and Hiver was just pretending to be him. He called her out, and she left only to show up a bit later as a Mesprit and pretended once again to be someone else, but this time, Quartz saw through it right away and re-caught her. She did say that Spes was not a perfect vessel, though; he was somehow still able to fight back.