This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Pokémon Live!
MechaMew2 is seemingly unaffected by any attack, no matter how strong.
Giovanni's song "It Will All Be Mine," featuring a performance by Darren Dunstan—who would later VA Pegasus in Yu-Gi-Oh!—and marching Rocket Grunts.
The MechaMew2 robot looked◊ awesome and terrifying.
Giovanni's threat to Professor Oak when he asks to hurry up and show him Team Rocket's achievement.
Giovanni: Always in such a rush, Professor. You really should learn to relax. You'll live longer.
Giovanni's songs often have creepy instrumentation, and can function as Jump Scares on the soundtrack.
Giovanni's Dark Reprise of "You and Me and Pokemon" starts out with a scare chord and details how once he defeats Pikachu the world will fall before his might. The song was even used in a Death NoteAMV.
One more/Won't be much longer til my/plan is complete! One fight/Then after that/You'll all be at my feet!
According to Professor Oak, the Rockets carried him and Delia away by dangling them in cages from a helicopter. Imagine that and try not to get vertigo.
Giovanni decides 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.
MechaMew2, upon becoming sentient, puts Giovanni in a headlock and prepares to blow up, with a timer ticking down. Even though MechaMew2 is good by then, it's still pretty unsettling.
Mewtwo wipes Ash's memories of his appearance for no apparent reason. Given that this happens after he hits MechaMew2 with enough of Ash's memories to make him faint, it may have been accidental.