Okay, for starters, putting your entire thread as a JPG is unnecessary; we don't need the real deal banner on the left. Cheers.
Your giant Pokéball is shaded horrifically badly. If there's a glow on it, there's no way the light source would be a band. In contrast, the shading on most of your trainers (although a few are clear edits) and fakemon seems fairly decent, but outlines that are too light (Moltra, Halongel), poor linework (Cymbal and the green owl) or poor concepts (Moderost) are letting you down. Badly. Kangabox is excellent, but its eyes, as with a lot of sprites, could do with being more cartoony, and less black. Look at other mammalian sprites for some ideas.
Onto the text. I'm not entirely sure I'm interested in the game's history, but I suppose it's a fine place to start. However, I'm seriously not interested in hearing how committed you are. Instead of saying you're at 12.5, work on the game and prove it. It's just blab otherwise. Concentrate on one thing, whether it's this game, or your tileset project, or your Sinnoh remake. Overstretching leads to boredom, lack of energy and apathy for your work, and, believe me, you won't have any kind of success that way. Start small and build on that.
I like the idea of incorporating magic. It seems like it could fit, but it seems bizarre that you've decided to add time, space, sound and light as new types, which are completely irrelevant to this concept. It's unnecessary bloat. Unless you're going to reinvent the battle system to suit these (which I wouldn't recommend), I'd steer clear of these.
Your story has a contradiction in it; the government clearly isn't resting on its laurels if they're being so uptight and forceful that the people are getting irritated. That literally doesn't make sense. "Knights of Shade" don't sound like thugs, either. They sound fairly organised, and look it, too.
I'm not at all convinced by your starter idea. Two each? I'm almost guaranteed to pick the water or ground one to combat the rival's Moltra, and then another, say Cantou, to take out a grass type that he might pick to compensate. It seems horribly unbalanced and uncontrollable. If you had a choice of six, with three from two different triangles, then that might be intriguing, but you need to think about this one a lot more.
While the "fragments" idea sounds good, borrowing off the anime's concept of gym challenges, I'm not sure I like the sound of adding an extra ten or twenty key battles by way of tiering. Sounds a bit repetitive, frankly. More diverse challenges sound more interesting, though. Is it a case of tackling only 8 of the leaders, or do you need to beat them all to collect all the fragments, out of interest? One sounds much more appealing than the other.
Badgium sounds corny, but the actual backstory to it is clever. I'd like to see more of a "there's a gap, so people apply" rather than your system which allows anyone successful to become a leader, regardless of whether there's room.
The mock-ups look good, but the grass palette clashes slightly, and the blue dome in the lab/headquarters thing on the left needs some work.
Okay, there are my thoughts. I hope they're helpful and constructive.