Suicune, despite the fact that he's the first Big Damn Hero other than Mew and Celebi to not speak human.
Team Rocket gets to be threatening as they actively help the Marauder in the first act of the film (even if it's not so much).
What about when Onix smacked a Tyrannitar right into the middle of a lake?
Considering than Tyrannitar is a pseudo-Legendary (at the time, only the second ever introduced), and that this one was power-enhanced by the IMM's Dark Balls...yeah, it counts. A lot. No wonder it evolved into a Steelix later down the line (albeit offscreen).
How about Bayleef defeating Scizor? Let that sink in...Bayleef, a second-stage grass type beating Scizor, a fully evolved Steel/Bug type, both of which resist grass.
The Marauder's giant tree-beast thing is very impressive CGI for the time.
In the Climax As the Marauder grabs Celebi one final time and attempts to blast away on his jet pack. Ash and Pikachu grab onto the Marauder's leg to save Celebi as he rises higher and higher. Ash then orders Pikachu to thunderbolt the evil man's jetpack, causing it to explode, sending all three plummeting several meters towards the forest floor. While the Marauder continues his long fall, Celebi saves Ash & Pikachu.
All of the forest Pokémon giving the Marauder his karma at the end of the film. Special note in that Caterpie and Weedle are the first to make him pay.