Nice story! The ruins link to the history of the Pokémon world, like Pokémopolis, and the jungle setting remind me of the beginning of the first Pokémon movie. Like you said, the intro had the look 'n feel of a Pokémon movie opening scene.

I found you being very good at portraying "Our Heroes" (a feat not easily accomplished), and at just making the whole story seem like it could be part of the anime continuity. I'll have you know the last I saw of Pokémon envolved the Battle Frontier and the Giant Butterfree event, and the fact I can't distinguish much between actual and imaginated references to Sinnoh events speaks for the genuine feel of your story.
The scene opening sentences are a good idea too, for setting up both the time and location of the event.

Not that you're in lack of shipping material, but I wonder what Ash's newfound "mature" thoughts might lead to should he ever farther down the road meet up with Misty again, her being the gal he travelled with the longest (through 3 Leagues, after all).
Aside from that, I'm hoping to find out how long before Chapter 1 the Intro was set, and how the Pikachu's will interact if and when they meet.