Yellow buildings: I don't see the problem with the windows as they blend naturally; the spacing is a tad off, I agree, but there's nothing I can do about that.
Grey Houses: I don't see the problem with the doors being in other places. The windows/extra space was made specifically for the purpose of having the door fit in other areas, so as not to be repetitive.
Blue Sign: I purposely changed the color on this tileset so as to make it look better [in my opinion; it is my map after all ] and I don't see an issue with it being blue.
Gym: This town isn't meant to have a Gym; it's not necessarily a town made just for Pokémon, and I didn't really want to put a Gym in it. I don't see how that contributes to it being unique considering most towns in a game have Gyms, but that's what opinions are for.
Thanks for the input :D Appreciated.