Hope you guys enjoy it, this is all I've written so far:
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   Today, the new transfer student came in. A red head with a wooden 'x' shaped bag on her back. As she took her first step a thump, followed by, "Ah," could be heard from within the bag. After her third step, she turned to the bag and shouted, "will you quiet down in there?"
   "I can't breathe in here..." returned a voice from inside the weird bag. After a quick apology, she opened the bag and a red mist came out. Followed by the mist were a few magic seals: A red star shaped seal, which indicated something forbidden. A blue quarter moon shaped seal, which meant something was shut inside for good, and a yellow heart shaped seal, which meant something unsettling had occurred. Before the smoke had cleared, coughing and mumbling could be heard coming from within the smoke. "You plan to do me in one of these days, don't you?" came another voice from inside the smoke.
   "What!? No! Why would you say that?" cried the transfer student. As the smoke finally cleared, a glossy red heart attached to the bag, and a blond haired cutey, standing chest forward were at last noticeable. Suddenly the room filled with awe and ooh, "Florina, what's the meaning of this?" asked the teacher.
   "Umm. Well," she took a step, taking somewhat of a sophisticated stance, "as you can see, I have successfully performed the-" before she could finish, a wave of disbelief was heard across the room. As if dealing the last blow, "Successfully, hmm?" finished the teacher.

I'm not sure if this was mentioned before, but here is a small idea that might work.
The possibility of having more than one storyline...
Maybe if choices the player makes as he/she goes along can change the outcome of the ending he/she gets?
Or perhaps storyline changes depending on which Pokemon you pick as a starter?
Of course, there could be the "no storyline," depending on the players' desire to follow up on the story? In my opinion, you shouldn't HAVE to follow the story to open up new paths.


^^^^
Maybe I should retract that idea? Not sure how the storyline works, even though I read it over twice x.x 
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Now I'm not sure how you guys have it set or want it to be, but do HM/TM's come from winning against trainers? Are they in pokeballs floating about the continent? Or do we have to talk to random NPCs to acquire them?