Sorry for the late reply, it was late in the evening when I remembered to check my inbox.
Emphasizing the protagonist is important but not constantly needed. With one light color and one dark color, the design helps itself in most backgrounds. Again, the player just needs to know where their character is on the screen.
You can keep vivid buildings as long as they're distinct from the protagonist and other objects/characters. Earthbound 3 has vivid buildings as well, but the characters have black lines around them so they don't blend into the background.
The robots can still have noticeable colors but do avoid using colors that can be confused as the protagonist's. You can still use blue for example, but you could resort to a more purple-ish blue or a less saturated blue. Just remember light, saturation and color can be helpful in indicating what's important in a scene. Like how pokeballs with items in them are vivid red even in a cave.
And the caves' ground would benefit from some kind of seamless, non-intrusive pattern to become more interesting.
I used to draw with paint net as well but nowadays there are more art programs available.
I now use paint tool sai 2. I selected anything other than the protagonist, rocks and tent, and applied a layer set to "Color" with brown over the selected part.
I recommend firealpaca, or even Krita for a free alternative if your computer can handle it, in mine it's a bit slow but gets the job done.
I'm off to sleep for now, I'm on a different time zone but feel free to leave a reply whenever you want.
I don't often check itch io but I do have a deviantart account with the same name, but without the exclamation point in this username.