Friend to All Living Things: Ash is a friend to all Pokemon, which is lampshaded by Misty in "I've Got A Secret". His memories and pure heart even wreck Giovanni's plan by giving MechaMew2 knowledge of love and right and wrong.
Good Morning, Crono: The story starts with Ash sleeping in at home and Pikachu shocking him awake.
Nonchalant Dodge: During "You Just Can't Win," Giovanni tries to punch Ash, who dodges and taunts him about it.
Ambiguous Gender: Surprisingly averted. Pikachu is repeatedly called "he" instead of "it" (probably because the song "Pikachu (I Choose You)" has Ash refer to it as being like his "brother"). Pikachu wouldn't be confirmed as male for several more years.
Demoted to Extra: Due to the limits of the medium, Pikachu is demoted from his status as a core character. He just pops up once in a while to make noises and prove he hasn't been Adapted Out.
James stands up to, and insults, Jessie more than in canon.
Jessie is a bit more upbeat and campy than in the anime.
Ambiguously Gay: Surprising for a show that shipped Ash/Misty and Giovanni/Delia, it doesn't reference James/Jessie. Instead we get James being as camp as ever and joking about "Don't Ask, Don't Tell".
Godhood Seeker: During "It Will All Be Mine," Giovanni says he'll have divine power and make the sun shine on only him.
Luke, I Am Your Father: Subverted. It's implied he's Ash's dad, but this is never noted explicitly and it's unknown if Giovanni even knows he has a child (judging from his lack of reaction to Ash and his attempt at killing him, he doesn't).
Near-Villain Victory: Giovanni's plan works completely, and he tries to kill Ash and Pikachu with Hyper Beam after they served their purpose in his plan. If not for Mewtwo's intervention, he would have won.
Visionary Villain: Giovanni claims his plan will change the world forever, and his villain songs describe ruling the planet and controlling each day to the point that he'll make the sun shine on him alone.
Would Hurt a Child: Giovanni is perfectly willing to kill Ash with MechaMew2's Hyper Beam, and he engages him in a fistfight shortly before that.
You're Insane!!: Delia calls him "mad" when he explains his world domination plans to her.
Composite Character: MechaMew2 is primarily based on Mewtwo, but also has Mew's unique feature of being able to learn every Pokemon move.
Invincible Villain: MechaMew2 wins every battle it participates in until the very end, meaning it defeated at least 250 trainers offscreen. It's only defeated by Mewtwo giving in sentience that results in it blowing up to stop Giovanni.
Nigh-Invulnerable: MechaMew2 is seemingly unaffected by any opponent's attack, no matter how strong.
Voice of the Legion: MechaMew2 speaks with heavy reverb and a male/female voice similar to the Mewtwo/Nurse Joy example from the anime's first movie.
Portrayed by: Dee Roscoli
Adaptational Backstory Change: The play predates the third movie and thus presents a contradictory backstory for Delia. Here, she was a part of Team Rocket as a teen. In the anime, it's shown she was a student of Professor Oak's as a teen.
Teen Pregnancy: This is alluded to. Delia was a Rocket member as a teen. It's never mentioned when she had Ash, but there are some implications she had him young (especially if he is Giovanni's son). This is canon to Pocket Monsters: The Animation, where Delia had Ash at 19.