As I've mentioned several times in the past, my brother originally came up with the concept, and looking back, he's made so many mistakes that I'm glad to have more or less completely eliminated them by this point in time. His main idea was pretty simple, really: make a story that's kinda like the anime, except darker and with a more complex plot. In the end, what he really had was the main character competing in the Jouto league, then travelling to Kantou, Houen, and the Orange Islands just for the hell of it. He tried to redeem this by saying that the league thing is just a side-quest, and it would mainly focus on the darker plot with the Rocket Gang (thing is, he actually thought he was being original with this... apparently, neither of us ventured much into the realm of fanfiction :P). What's sad is that I actually decided to go along with this as I was writing the first version of the fic.
Over time, I decided that having the main character go through the other regional leagues past Jouto was kinda pointless, especially as my brother didn't originally have much planned to take place in them (and it likely would've done nothing except make the story drag out too much), so at some point, I decided to scrap them (though, I might still use some of the other continents in the story for completely different reasons). I must've made that decision sometime while I was in the middle of writing that first revision, actually, so by the time I wrote the script, I'd already decided he'd travel through Jouto and nothing more.
However, some implications arose as I was writing the script: I found myself still changing my mind as I wrote it out. At first, I just wanted to convert the old narrative into a different format, but as I looked through the narrative again, I saw many things I thought could need changing; for instance, my brother used a cameo, Kenta from the Crystal special, as Hiro's travelling companion, but he ended up being damned pointless to the overall plot. There was also a scene where Hiro and his friend, Chris (another character I'm going to scrap, since he was just based off my brother's friend in real life and he never did much for the plot either), went into the Burned Tower, decide to clean graffiti off the statues of the legendary beasts, and they came to life and ran off. Really, my brother had plans for a lot of game events to take place... obviously, I decided I didn't want to go for a clone of the games with a darker plot involved, especially seeing as the game protagonists are kinda big Deus Ex Machinas (though with the games, I guess it's excusable since the programmers had to make things convenient for the player. I mean, how are you supposed to collect all the Pokemon if legendaries are untouchable? Not to mention always just happening to be at the right place and time for a scenario to take place for you to witness, with no real explanation other than chance).
[cough] But I digress. For the first couple of chapters, I tried to keep these changes from the first writing rather minor, but then by chapter three (very end of chapter 2, actually), the rewriting got a bit more extreme. I finally decided that I should do away with the whole badge quest altogether, as it really had no connection with the overall plot in the first place (and it's not as if Hiro seems like the type of character who'd wanna participate in a competition). However, since the foreshadowing of the badge quest still lingered from the first couple chapters, I had to think of ways to improvise (if you'll notice, this is actually apparent at the end of chapter 2. I finally decided this immediately as I was finishing the chapter. In the narrative, Hiro got pissed off at the teacher and, despite not being interested in Pokemon before, suddenly decides to leave on a journey since nobody believes he's related to the Eievui sisters and he happened to find an Eievui of his own... which in itself sounds like pretty corny writing, if you ask me. At the end, I had Hiro look at the Pokemon Center, just about ready to write it to make him decide to leave on the journey, when suddenly I started typing differently and made Hiro change his mind just as I did).
To continue on with this while using a somewhat logical excuse (and I guess I can use spoilers now, seeing as I'll be dropping most of this in the next, and hopefully final, version), I was going to have Professor Utsugi's assistant (the fisher lady) shadow Hiro while trying to persuade him to actively participate in a badge quest in order to keep him moving and hopefully avoid the Rocket Gang (Utsugi feared the possibility of him being tracked down if he stayed in one place, but didn't want to outright tell Hiro about the situation), and thus avoid their capture of Hiro's seemingly special Eievui (in actuality, Kiryuu didn't say a thing and the rest of Rocket Dan was none the wiser). The plan would go up in smoke, however, when Hiro, upon being persuaded to participate in the first gym, immediately loses interest and just tries going back to Enju City (he'd also eventually come to the conclusion that the road blocks were intentionally set against him, causing him to plow past them and continue on his way... that, and he'd have another run-in with the Rocket Gang, one which would garner attention from the entire organization). By the time he returned to Enju, I was really hoping to have the story get on track and leave the gym quest behind for good, but unfortunately, I quit writing the script before I got that far.
Now with what I have planned for the manga, I hope to never even use a badge quest in the first place and focus purely on the main plot and characterization. However, some things are going to remain: the renamed main character will travel to a few places in the old version (except it's not exactly journeying; he'll have means of getting there more instantaneously rather than spending time on foot, and he'll be in such places for entirely different reasons and so that certain events I wanted to keep can still take place), but for a good portion of the storyline, he'll remain in Enju City (and I'll probably stick with his disinterest to become a Trainer, probably not even have him catch anything besides his Eievui). When I really think about it, the main character's relationship with the five sisters probably could've been omitted as well (I think my brother only did that because the connection with Eievui, and he was giving an Eievui to the main character in the first place because his favorite Pokemon is one of its evolutions), but I decided against it because I've rather grown to like them, as well as the personalities, unique from any other aspect of the franchise depicting them, which I've given to them over time. However, I don't want them to rot as useless, pointless characters neither, so I've slowly came up with ways that they could play more active roles in the plot (really, I was trying to do this with the script fic as well, but I couldn't think of too much at the time).
Speaking of trying to tie characters I like into the plot... in spite of the lack of traveling involved, I'm definitely gonna work the fisher woman into the revision (I actually had it planned in the script version that she'd be playing major roles later on), and I also enjoyed the chapter with Michie (the last script chapter that I wrote), so I'll figure out some way to work both her and the one-sided romance into the manga. There was also a comic relief/ecchi character that I, by chance, came up with on the spot as I was writing the last two chapters of the narrative version before I called it quits (I'll be surprised if anyone here happens to know her, seeing as I only posted the narrative on SPPF and fanfiction.net, with the narrative being pruned from the former and the later chapters not even being posted on the latter... I also posted the narrative here for those interested in seeing how much I changed things, but I gave that up after the first four chapters. If you do happen to be familiar with the last parts of the narrative, please PM me and don't spoil anything here). Not only did I intend to retain her in future revisions (it's a shame I couldn't get around to debuting her in the scripted revision -_-), but as I came up with her scenarios, I grew to like her so much that I've now got plans to have her participate as a major character later on, rather than being restricted to a comic relief role. Also from the late chapters of the narrative was a one-shot drunkard from Rocket Gang who was seeking a promotion... though he was absent in the script version (and I wasn't planning on using him at the time, neither), I'm now gonna go back and turn him into a bit of a recurring character (with a couple important roles as well). In the manga, you can expect to see him appear rather early on (even before Kiryuu first appears).