Okaaaaaaaaaaaaaaaaaaaaaaaaaaaay. Finally got caught up with this. That took far longer than I expected it to.
Just going to start by echoing the whole 'pay more attention to grammar' thing. It got better, for a while, but it slid downhill a bit in recent chapters. On a related note, in the last chapter you oscillated between calling Chigon a male or withholding any reference of its gender. The Generation One Gender Neutral schtick really only works if you keep it gender neutral. Otherwise it just seems strange.
This story has a very anime-esque feel. Not necessarily a Pokemon Anime-esque feel, but it genuinely feels like a faithful adaptation of an anime with the common tropes, setup, and some of the writing. Because of that I can forgive your use of deadpanning, but another word really bothers me. 'Sagely.' I generally apply this to older men and monks giving deep, philosophical advice. It pops up all the time in this story referring to teenagers and teachers talking about battling, superficial relationship details, and caring for eggs. The rarity of the adverb and its connotations really don't mesh well with its intended use. I would find another adverb or just go without one in those cases.
And now that general grammar rant is over, onto actual substance!
Once again, I view this story as an anime adaptation and will review it as such. Because of this I can ignore the prevalence of tropes that would be very questionable in other stories such as the prevalence of deadpanning, random tournament arc buildups, overpowered enemies of the week that do crazy things no one pays much attention too. *cough*BlackKnightsDestroyAMajorCityWithTheHelpOfLegendaryPokemonAndTheIncidentIsSeldomSpokenOfAfter wards*cough* Sorry. Long coughing fit there.
I also didn't read the first story, so I wasn't really that impressed with characterization early on to be honest. We have the Powerful Loner Friend, the Shy Booksmart Nerd, the Perverted Lancer, a generic hot anime teacher, and no one else is really important except for Reggie for most of the story. Even Reggie's Underwhelming Chosen One role is hardly unique given... early anime Ash.
That's not to say that characterization stays generic. Fin has some alluded depths and becomes more of a steady lancer as time goes on. Anime teacher is minor enough it doesn't matter and is getting more development now. Darren... is still the same but I think that's the point of his character. Miko actually became important in this story and is notable for being a Primary Harem Love Interest who can fight and takes romance stuff into her own hands. Valerie is similarly reasonably developed for a supporting character. And at one point you really start to deconstruct the loser hero hard, which was a nice twist and actually started character development for Reggie which was nice.
And then we get to Kevin Samuels.
I will forgive any characterization gripes I have about this story because of that guy. I called him Jay in my inner monologue, because he really struck me as an evil Gatsby. Which was fantastic. Especially at the end when he went from smug competitor to total, complete, gutsy monster of a manipulative villain. Just... I love that character. I really do.
So if that's characterization and storytelling out of the way, onto the plot itself.
To be totally honest, even if you never told me this was a sequel and claimed that all of the events referenced are some grand backstory that you slowly explained as the narrative wove on I would automatically think of this story as the middle of a trilogy. There isn't really an overarching plot, which is kind of acceptable because it really is a slice of life anime, but then at the end it starts to build up to another event. The Memento Mori happen, but they're kind of there in a "here's a big bad lurking in the shadows while the heroes train to face him... IN THE NEXT STORY!" The Enforcers are there, but that's a pretty petty obstacle for a group heading from an apparently near omnicidal maniac with ancient powertech into a powerful league of assassins and criminals. So... it's kind of an entire breather story that facilitates a sweep from one story into another one, which is a typical problem with middle installments in trilogies.
To be fair to you, the plot you do have was handled very well. The romance arc in particular was nice and led into Evil Gatsby's part of the Enforcer's arc well. There just really wasn't any sort of a compelling background story guiding things along, except one that was apparently mostly just sequel setup.
In short, there were definitely parts of the story that I thought were admirable. I will always remember and cherish Evil Gatsby, and as the Bug Gym Leader on Smogon's ASB I appreciate the Genesect love. Characterization got better and the plot is certainly not bad, especially given the unfortunate position as part two of three+ it finds itself in. But from having not read the original I thought that starting characterization was pretty reliant on archetypes and the plot as a whole was kind of aimless and meandering.
So... I guess I would say the early story was above average. The middle and later story are distinctly good.
And that's all I really have to say about that. Add me to the notification list, please.