Some tips for painting a map by hand...

Large file size: Paint it mostly zoomed out, so you get the whole picture; high resolution also helps keep the image from becoming pixelated; using as large a brush as possible for your details keeps it smoother; if you need more detail in a specific area - don't use a five-pixel-wide brush - use the rectangular selection tool to grab the spot you want to define and copy it to a new file, enlarge that image 2-3x and use the bigger, smoother brush to make it all fancy before selecting the whole thing and shrinking it back to the original size to copy back into the original place on the original map.

You might try painting your map in grey-scale, so the values (light to dark and everything in between) remain solid and pleasing to look at. Things won't jump out as much. You can overlay color later on if you want to, on a different layer, or more, so you can play with many combinations to get the best look. Also, if you start with a mid-grey color as your background instead of white, any show-through will be less jarring.

Composition and space: Your map, at the moment, feels squished, since you have so many smaller areas of interest at the corners and edges. Give it some breathing room.

Shading: If you depict your map, especially top-down, as if the sun were shining from closer to the horizon (shadows on the opposite side of things), you'll give more weight to the shape of the land and buildings, etc.

That should be enough to start with. =)