As a fellow PokeSpe fanfic writer (*cough*Obnoxious Fate*cough*) and in the process of writing a multi-novel original story, I think I can shed some enlightenment on the process.
-how do you start writing a fic? Like, a specific type of scene. Silver getting off the boat, Silver finding Soul laying on the ground, etc.
One little trick that works for me is that I find one or two scenes that is the centerpiece of the story and then I ask myself "How do I get to this point?"
For example: Obnoxious Fate deals with the idea that Wally feels like he's been missing out on the funner things in life (like going to the Battle Frontier) because of his illness while his doctor is a scumbag who is in debt to the Sinnoh mafia. The two scenes that I felt were essential to the story were "Emerald Meets Wally" and "Doctor faces Dexholders". From there, it was a matter of "How can I make Wally and Emerald meet?" and "How do I get the Dexholders involved?"
I wouldn't start with Silver getting off of the boat, per say. I would maybe start with Silver on the boat while a conversation between him and someone else (like one of the other Dexholders) gives us exposition and lets the reader know what's going on (the kiddnapping) without being too obvious. Then Silver gets off of the boat. Like I said, find out what you want your arc to accomplish and worry about getting your characters there while keeping them in-character. The awesome part comes when you find yourself writing dialog and actions without even thinking. Almost like the characters are telling you what they would do.
As for the villain, maybe the guy who kidnapped the Viridian trio has some purpose that in his head is 100% morally correct while coming off as completely insane and ludicrous to everyone else? I'm at a loss for this one. This is something that you'll have to figure out as you build your story brick-by-brick.
Any other questions?