Hi IAteAPlane, I moved your thread here since it is a webcomic, though I realize this section has been very quiet! I'm more accustomed to reviewing fics and fic ideas, but I can certainly try to give you some feedback on what you posted here!
For starters it sounds like you have a lot of cool ideas in terms of world-building! It's definitely important to have a clear idea of the world you're setting your story in, because the world affects the people, the way they act, and the way they live. It sounds like you're very ambitious and have a lot of ideas, which is always great when starting a new project! That said, while you've told us about how you want the explore economics and politics and the themes of companionship and loss, and include plot points like a Champion manipulating the Elite Four and a morally shady professor, you haven't really said how you intend on portraying all of these things. You have some basic ideas for what the protagonists' journey might look like, but it doesn't sound like you have a concrete plan on how you would execute either of them.
Additionally, every story needs a plot to carry us through the world you've created, but right now it's unclear as to what that plot is. You have two outlines right now, but neither is very concrete. Since both of your outlines are pretty vague, it's hard to say which would be better at this point - you might want to reflect more on each one, fleshing it out and thinking about how realistic it would be to do it. That would definitely help you make a decision!
Ity's also difficult to give you any feedback without some idea of who your characters will be. You have an estimate of how many characters you might have, which can be helpful, but who exactly are they? What are their goals, what are they fighting for? Generally you create the characters first based on the needs of the story, rather than using a predefined number as a guideline.
Also, be careful not to create too much work for yourself! I quite like the idea of type-swapped Pokemon and new evolutions, but it sounds like a lot of work, and I wonder why you need to do this in the first place. Is there a reason that Pokemon in your region have unique types and evolutions? If it ties into the plot somehow that would be very cool, but is this a central part of your fic?
I know it's a lot to think about, but you have a lot of ideas going on here and I wanted to give an idea of things to think about before going further. It sounds like you have a lot of cool concepts, you'll just have to figure out what to include in the final product. I hope this helped, good luck!
~Psychic