I'd say first figure out what your main draws are-Gameplay, story, fakemon, etc. Then, from there, start forming a general idea of major locations. (A hub for a certain kind of gameplay, the major story locations, habitats for your fakemon, etc) I would put setting after your main draw, because you don't want to write yourself out of something you really wanted to include. Like, say you designed your region completely, and it doesn't have any icy locations-but you have all these Ice-types you want to put in! Now you have to try to rearrange your map to fit in an ice area!
This might be counter-intuitive, but I'd say put your polish/flourishes/quality of life things in
first, before you even start mapping or eventing. That way, you can make sure nothing you add in is going to be broken or need updates from it. Maybe you want to add
Mr. Gela's name windows to your dialogue-put that in first, before you start making all the events with dialogue, or you'll have to edit every event again later.
After that, I honestly think it's just a matter of what you want to get done? If you're working with a deadline, like for the Game Jam or something, then you should definitely start with the beginning maps and events before going on to the next, so you have something playable. But if you're releasing your game whenever you want, who cares what order things get done in? You could get a map done and save it to be evented later, you could get an ability designed and save the fakemon for later, etc. Only rules I can think of there would be
- Don't make events move before the map is ready. (so you can be sure their movements are in the right spot)
- Don't include fakemon before their moves/abilities are working. (so the game doesn't crash when you test them out)
- Don't make trainer battles until you've included the fakemon (if they use them)-the game will crash crash without them
- So, pretty much, don't make something new that relies on something else new if it's missing?