well, PMC started as my brother's idea.... I guess what he was going for was extremely basic. He took a couple of his favorite Pokemon, and made some kind of conflict involving them, and I guess took advantage of some canon things that are associated with one of his favorites (the Kimono Sisters). He wanted to make it dark, too, because of the anime being too light-hearted, with an actual plot instead of an episodic formula. Of course, this was back when the Jouto saga was still airing in America, and who wouldn't get sick of all that crap? Nowadays.... I forget exactly why I wanted to take over when he abandoned it. Perhaps I was extremely shallow at the time, and thought just anything dark and action-packed would be good. Maybe I saw potential in a franchise that involves carrying ferocious beasts in portable containers, a potential being totally wasted on the same basic storylines about "being the best competitor" and whatnot that the anime and games give you, despite how such storylines mix in terrorist groups and other potentially deadly antagonists. Perhaps it was even because doujinshi intrigued me enough to warrant trying to make one myself, I mean, a simple fan could potentially make something similar to the great commercial manga we see everyday, and not even have to bother with licensing and such. That abandoned plot to start off with just helped jump-start my interest in that even further (at the time, I'd recently bought the first two DVDs to Comic Party, which may've also had an effect).
Whatever the case was, I had a plot outline for a future doujinshi I still plan to work on. As I said, I was pretty shallow at the time and just thought anything dark was cool.... though, I did put some consideration into drama, adding onto what my brother didn't have, but not much. If I ever do a doujinshi, I'd like it to have a story similar to the kind we see in most well-acclaimed official manga, and, well..... over the years, I've been kinda taking in info on what makes a good story through various anime reviews and people's comments and observing existing series and such, taking note of the deeper things that I never really gave much thought to at first and how pretty much all these series make a good point about whatever theme or message it's trying to convey (ironically, my English classes barely did s*** for me). Now, I took that original basic plot of my brother's, changed some things around, removed some unnecessary things, and added a lot, particularly those afforementioned deep things that make all the characters and events seem 3D (though sometimes, as you may see in a future chapter, I'll think of a character I really like, add them in, and kinda plan out what role and backstory they could have only after I do so). I still feel as though I'm struggling with some characterization for the antagonists, and I'm wondering what more of a role my minor characters could play, and considering I basically picked up on writing someone's idea, I still don't quite have a clue on the main theme as of yet, but other than that, I think I'm doing alright.
And.... that was just PMC. Now, when it comes to my (not my brother's) original works, stories I plan to write in the future (also with the intend of future doujinshi).... I guess I kinda thought of interesting characters first, placed them in some setting, and built on from there.