This is a random idea I wanted to bounce off somebody before I got too into it. It may be too standard, I dunno.
So we start out with a dreamy 'leap before you look' kind of hero/heroine. S/he comes from a normal kind of place (for the Pokemon world, anyhow) and is a huge fan of TV shows, movies, and comics that glamorize the travels of Pokemon Trainers. S/he decides that s/he wants to be one of those glamorous Trainers, but his/her parents say no. Probably because they know about his/her chances being slim for success.
But the kid decides to run off and becomes a stowaway on a ship. The captain is amused by the kid's plan, saying he was like that as his/her age. So he drops the kid off in the Jasper region at the town where the Professor lives. The kid's very excited, but not certain of where to go, checks with the Pokecenter. The nurse seems worried, but goes ahead and tells him/her where the Professor's lab is.
Then s/he meets Professor Ned. Now Ned is a batty kind of guy. He won't do any work unless everything is just so, then works for days on end without coming out of his lab. The hero/heroine starts becoming worried, but offers to work as Ned's assistant. Ned agrees and puts the kid to completing apparently meaningless tasks.
Eventually, the hero/heroine starts hinting that, say, wouldn't it be nice if somebody took a Pokedex and went out to catalogue all of the Pokemon that lived in Jasper? Subtle hints don't work on Ned, but the message gets through and he likes the idea. He agrees to set the kid up with all the things necessary to become a traveling researcher.
At the very last minute, he finally remembers the starter Pokemon. The hero/heroine hopes for a choice of three, but then is simply given one. This Pokemon is apparently Ned's special bioengineering project.
He gives the kid a strange warning about the starter, then sends him/her off on a journey that is anything but glamorous.
The starter is one of my fakemon and is so for a specific reason. The readers know as much about the Pokemon as the main character does, which is almost nothing. The warning is to not let it set itself on fire, as it's a Grass type, but eventually gains a secondary Fire type. It's a flowery sort, which means it would match a girl, but would be funny with a guy. The journey will likely be a failure as far as Gyms go, but hey, that's how most unwritten journeys go, right? I'm thinking no legendaries, but maybe a disappointment in that lack.
Any kind of comment is welcome.