Okay, well I'm going to write this up and post it now. It might sound like I'm yelling at you or trying to tell you what you have to do in the sequel, but I really am not trying to sound that way. I really just want to put up some suggestions and give you some warnings. Mostly just all my collective thoughts from reading the past few chapters or so. Again, please don't take this too harshly.
Okay. So. First thing. I want to say congrats on finishing this. It feels like forever ago when I started reading this; back when Eclipse was the owner of the SPC. Wow. We were so different, as was this fic. And so much has changed. You're going to college, etc. I love the feeling of having been with this story for so long, and being able to see it finish, even if it wasn't completely to my preferences (but again, not my fic, so that shouldn't be taken like I'm telling you to always make sure I like it).
I just wanted to let you know that before I delve into the big parts of this.
Now, the review of everything. I liked the way this began when I first started reading it. iirc, wasn't one of the boys telling the Arceus myth thing? I think the image that the beginning scene made in my head - the one of four innocent boys just talking about stuff - made the story seem so much more relatable and real. The Prologue is okay now, don't get me wrong, I just think you changed it too much. I was just disappointed that the fic that started so innocently and with such young and happy characters (which later and at a nice pace grew into more mature characters fighting a serious war) had its beginning changed around so much.
Speaking of the innocent beginning and such, I love how this all started. Irregardless of how badly George and Joey were handled, I really did like the Gym Leaders you made, the setup of the Gyms on the Islands, and the journey where everyone was just having fun. I'm not even sure where it started changing from five kids on a journey to five kids fighting in a war, but the transition went at an excellent pace, and I seem to have forgotten that recently - it doesn't change my views on recent chapters though, so you know.
Moving on to the topic of your characters and their development, just watch out in the sequel. In my opinion, I think you should try bringing John back to the innocent character he used to be. Right now he's so depressing and literally gets on my nerves. The change of him maturing was nice, yes, but he went from a soft, squishy little kid to this hard, somewhat emotionless rock. Again, just in my opinion, watch out to not make him even harder. And if you want to take this advice, I also want to just suggest that you don't actually say that you're changing John back to be more innocent. It really breaks the transition.
I also want to suggest that you try taking peoples' opinions and suggestions more. It's one thing to say you can take criticism and then make excuses for things, but it's another to listen to your readers and radically change how your story goes. I know, because I've done just that. The Sapphire Story, in the recent-most chapter, wasn't at all the same. Changing the fic so that it appeals to readers and also to you will help immensely in gaining reviewers, and I think the reason you don't have many right now is because of that. Rviewers take the time to express their feelings about what they read, and when the writer completely ignores them about what they've said it feels like a cold slap in the face. Almost like "Hey, thanks for giving this thread +1 postcount, now I'm going to just continue on and not pay attention to anything you just spent time writing for me." :/ Believe me, all those times I mentioned George and Joey only to have nothing done until chapters later (which ended up being done in not the best way, imo) really made me not want to review. Which I did a few times. js. Make sure to really take into account what people have to say. I know you do read what we write and do change some things, but sometimes it has to be a bigger change than what you might like. Though you could probably end up liking it if you be sure to have fun with it.
In the sequel, try not to change the reason most people are reading your fic. Like in this fic, I'm sure at least eighty percent of your writers were here to read the journey of John and Lindsey and them trying to reach their goal of the League/GF. As things change primarily to the Galactic stuff, it got kind of dull- actually no, I have to be honest; it got really dull. I know you wanted it to be full of action or suspense or something, but ninety-five percent of the time it failed :/ ...moving on. Having the League and Grand Festival both end at the very beginning of them made the twenty plus chapters of Gym Battles and Contests completely pointless. No one wants to read all that only to have it ruined in the end - and I really mean that, it was so anti-climactic that it went downhill from there. The stuff you see as filler-y and somewhat pointless is usually a big part of why readers enjoy stuff. You have to establish what is completely off-topic to the plot and will bore your readers from what's only slightly off-topic but still makes your readers want to read.
In regards to John's new set of Pokémon (and I'm sure you know this already, but I want to repeat it), please choose what you're going to do with them ahead of time. Either name them and give them personalities or don't. It was annoying to have to reread stuff after you threw in all their nicknames and everything.
Oh. This thought just occurred to me: you should try to include more interesting filler/side-scene stuff in chapters. Not to be demanding here, but more actually begging. The filler scenes you have now are boring, what with the Harken scene in the chapter before last. Like really, not really anyone wants to read that kind of stuff unless it's the main characters doing it. In TSS I include tons of scenes that I could easily delete and stuff would still make sense, but it adds to the parts that make it enjoyable, and most things in this fic lacked that. Sorry :/
I don't like ending on that somewhat harsh note, but that's all I have to say. All my thoughts on this fic are out, and all my suggestions are mixed in. Please take this all into account, and if you hate me and want to make excuses or yell at me through PM, I completely understand. No one likes a lot of criticism, especially not this much all at once, but it needed to be said.
Once more, huge congrats and harrahs to you for finishing, and I wish you the best of luck in your sequel.