This would be great except some of the information is just flat out incorrect.
"Ampharos is the best fit to take down Lance." Wtf are you talking about? Even if you're going with ampharos-m, which you'd have to to get the dragon typing, ampharos is too slow to do anything and the type advantage works both ways. For that matter, Giovanni clearly doesn't know what you're searching for (the mega stone) so he has no reason to believe you when you say an electric type can beat Lance's dragons.
Proteins and braces work no matter what? These same pokemon are a month old. If anything, vitamins and braces would lose effectiveness over time, not continue to accumulate like you'd guess.
Flaffy, a yer old, can take on Erica's full team? There is no type advantage? Except you're wrong on both accounts. Grass resists electric attacks.
Hell, why would egg moves be scannable before the eggs hatch at all? Why would everstones work the way you think they do in breeding? You're blatantly ignoring type matchups from games but acting like game mechanics like breeding and natures matters for anything.
This had an interesting premise but turned into steaming garbage because you can't seem to decide whether to take a realistic or video game take on pokemon.

This is a fascinating fic, and I'm looking forward to more!

This is pretty interesting. I'll look forward to any more of your work if you decide to continue.