"Is it generally accepted to include something that was not mentioned in the anime or the games, and make it up in the fic (of course as long as sufficient detail is made)?"
Yeah, I think that's taken pretty well. Some people's fics aren't canon at all, while others state at the outset that their characters are in a new region where the rules are slightly different. So if you want to to tackle an issue that the Pokeverse doesn't mention, no one will complain. As long as you aren't flipping everything around, like saying that humans evolved from Pokemon...
I don't really know what to suggest, but the first thing that occured to me was just derailing the journeyfic plot. Young trainer grabs starter Poke, sets off on journey, gets some badges - and is suddenly distracted by something completely unrelated to Pokemon battling. It's a big world, after all. There's a lot of stuff to be distracted by. Maybe he/she gets persuaded by smugglers, or lost in the forest, or sent on a pointless quest across the whole region. Battling takes a back seat, but Pokemon are still at the forefront because they're kind of everywhere.
As for avoiding cliches, I think the biggest one is the first scene. You know, where the trainer-to-be wakes up, eats breakfast, and runs to the lab to get their starter. It's so tiresome. Skip that entirely and start the story "in the middle of things", say, at the first gym battle.
However, if your protagonist really is a rejected orphan who learns important life lessons, you have a lot to make up for. (I really hope you were exaggerating.)
dreaming again
of a train track ending at the edge of the sea