Ass Pull: Lampshaded and refered to by name when Pikachu is kidnapped by Team Rocket. Despite being broke enough to resort to stealing food, Team Rocket somehow has access to advanced equipment like headbands infused with dark-type energy and giant electricity-absorbing robots.
Badass Decay: Compared to Canon, Ash's team's performance against Gary (barring Latios and Charizard) is... embarrassing, to say the least. Against Gary, half his team is subjected to The Worf Effect (3-0), so when the 2nd half begins only Pikachu otherwise defeats any of his team (Umbreon), Charizard (who beats 2) and then Latios (who beats 3) are brought out. Granted the line-up Gary had was a little different, but it's still kind of disappointing
Subverted with the fight against Harrison - in this story, he's revealed to have a much more powerful team than that which he used in Canon, and breaks it out specifically to counter Latios. Even when he loses, it's played very plausibly.
Growing the Beard: The author's writing improved greatly around Chapter 7 or so when he got a beta reader, though it isn't until the battles of the Silver Conference start that he learns to Show, Don't Tell.
One-Scene Wonder: Everyone was pleasantly surprised when Lt. Surge appeared in the last chapter of the first story.