First off, love this idea. Can't stress it enough. Funnily enough, I had this idea for this before for a story, but never got around to writing it; using the PMD world as ideas for basically a parody of PxR peeps and wanky zany hijinx.

Second off, there's a lot of PMD comics out there. A lot. There are a lot of comics, in general, that star Pokemon and only Pokemon, too, humans known or not. I'm not sure if we really really want a super-different world, but I feel like while our own ideas may persist, I want something, just something, even just one thing, that puts this world as vastly different from other worlds like it. Which raises the question of if we really want to start worldbuilding early.

I do have a few ideas... And a few questions. I'll just state the ideas first.

-Make several Legendary Pokemon wholly fictitious but not all of them. By 'fictitious,' I mean 'In-game they are real, but in the canon we have established they are nonexistent.' This assumes we'll have Pokemon Religion play a big role or such, but it can still hole up some big surprises; this way, we could have several pantheons and local deities, some of which are filled with fake Legendaries, while others have Legends that actually exist (and some have both, too). This allows us to play the game of 'is this a real god-like being or just a poser,' and if we do say a lot of legendaries are just regular Pokemon posing as local deities, actually encountering a genuine Legendary (even one like Keldeo or Uxie) may be a huge boss-level deal, especially if they're not friendly. As an alternative, we could have a reasonably singular pantheon that works differently from standard Pokemon fare, and keep our focus squarely on a manageable group of Legends.

-Make the Pokemon square off against very unfamiliar forces. And I don't just mean other Pokemon or altered Pokemon either, or even Ultra Beasts-I mean things that very well aren't established in the canon of Pokemon. The most influential example I can give for this kind of thing is the Trials of Juno, specifically the local variant on the Legions of Hell, though we could probably do something else.

-Make anomalous Pokemon. By which I mean Pokemon of a kin to the Regional Variants of Alola, only on a much wider scale of potential. Like, a ridiculously giant Pokemon, or a Pokemon that is basically the merger of two Pokemon at once (including a Legend) or ones with implausible attacks (like Judgement on a lowly Bidoof.) Have the protagonist be anomalous somehow. Shiny, halfbreed legend, stupid-strong attack, or something else; something weird and very different, beyond maybe once being human.

As for questions, I really only have three:

-How are we going to potray the Mystery Dungeon enemies? Bandits? Hopelessly brainwashed victims of the Mystery Dungeon phenomena? Constructs of the Mystery Dungeon itself? Will we even include legitimate Mystery Dungeons?

-Are we going to focus on a core cast of characters, or a wide cast of characters? Like, how many secondary characters, protagonists and factions will we factor in? I believe that, with the way the Character Design Contest is worded, that we'll only have one major hero and thus a Primary Protagonist; but what about the Protagonists around THE Protagionist? What about his antagonists, for that matter?

-What's our Genre? This sounds simple, but it's not. Are we going to be like a Shonen Anime? Or are we (for whatever reason) going full Magical Girl? Sticking to the core rulebook? Full Lovecraftian dive or other horror? Romcom? Parody wherein the main character wields the almighty power of the stick of Rule 63, and wields Genderbending amongst his/her/their/tem/yes combat maneuvers?

My artistic talent is literally beneath the level of XKCD. It's not going to improve to a manageable level in any quick time period with all that's already on my plate. This is all I can help you with, but hey. It's something, right? I can help storyboard and characterize, if nothing else.