Yes the cliff/shore look rather bad.
Go to your menu Advanced and make certain the 'enforce water limits' is unchecked.
Then re-paint your water areas something that you know is different from land (texture) or repaint your land. If your water areas are already dirt, you most likely can skip this tedious process. I usually start off with all sand for water, this way once I make everything the same level I know where the water is.
In your terrain palette select 'same level' with no terrain texture, drag the land over the water removing all of the cliffs.
Doing it this way instead of starting out with all water will allow you to have higher points of land with higher water sources, thus you can place lakes, ponds with streams and water falls on your lands flowing down to ocean and lower bits of water.
If you have no plans for higher sources of water, then you can use your terrain took deep water, turn off the texture and covert everything to deep water, then raise the land up out of the water.
Once you have done that hit P (to turn on your pathing) then use the terrain palette tool Apply Height: Lower - use a single dot brush, lower where the water was until you get a blue dot. Raise that once click, then flatten your shore likes with the Apply Height: Plateau.
Then you can go back and lower the rest of your water until its either blue (walkable, not buildable) or pink - no building, no walking. then use the smooth tool to smooth it all making a nice smooth shore line.
This will also remove the default sand at the top and bottom of your cliff, allowing you more options for your terrain textures (grass, dirt, bricks, etc).
Where you have your starting units, you can still keep your 'wall' if you want to. I personally use the walls destructible, custom the size and then select and while holding down Ctrl I page down to lower it. I go back with pathing blockers where or when needed - if needed as a boarder to wall cliffs, it just looks cleaner.
If you want you can make a custom bridge, change its model to one of the walls and make it walkable, that way your wall is walkable as well and you can use the walls side by side on blue pathing water.
While placed units in the editor will be on the ground, in game they will be on the wall See my example below, in that I used the low wall end, made a bridge custom doodad, my well and my villager are placed on the map (left side hidden by the doodads) yet in game (right side) they are on top.
For my squares I changed the pathing to Circle of Power, and then carefully sized them to where the tops just met, I have several, what is shown is white and medium dark, the same model I just tinkered with the tinting (Art - tinting Color - red/green/blue) to get the look of different colored marble tiles.
You do not need a pathing for anything you make walkable, you do need to either change the texture beneath to a rock base unbuildable) and/or lay in pathing blockers around the edge where you do not want units 'falling' off.
Since your hero picking area is at a corner of the map, I would suggest putting in a wall of something to hide that it is in the corner of the map. further I would move it right and down (East and South) a square or two to get rid of that shadow line.
Some terrain height variation should be used on 'land' use the Height tools to raise some low hills.
While shrubs are useful, they do not really fill in the landscape. Make a couple custom 'rushes' then change the color tinting to shades of green, clump them together to where you get a darkgreen a light green and a small brown 'grass' variation (not the hideous cattail thingy) you will have a decent living tall grass look. Use all brown where you want dead grass, use mostly greens where you want life.
Also think about making copies of your trees, ones with smaller ranges of scale, smaller pathing and less hit points - these would be 'seedling' varieties of your trees - it tends to make the map look nicer and more realistic having smaller versions. I have used Ashenvale and Felwood tree walls reduced in size to make hedgerows.
Personally I start out with Ashenvale tileset then go advance and modify the set, I usually remove things like the leaves and vines, rough dirt and use other tiles from other sets. I personally do not like the grass from the sunken ruins, I prefer the grass of Ashenvale, its color and brick/stone overlap is better. I know you are aiming for the sunkenruins look but I suspect you can do it with different tiles. Dalaran ruins ruined marble is placed here and there with sand or Ashenvale grassy dirt looks like granite (if used sparingly)
You can modify water color through the Scenerio/Map options - however I suspect that if you just use the lower tool and lower one point brush until it turns pink, then Plateau tool the watery depths out at that level you will have nice looking water for the game.
When it comes to buildings and unit buildings I increase their sizes, use the next size up pathing map. Buildings in WCIII are always way too small and look unrealistic.
With most of my neutral buildings I just remove the foundation (Art - Ground Texture) and use the terrain textures, it can look a lot better that way.
Weather: Use regional weather, keeping your hero picking area 'fair and sunny' and selectively using heavy rain and light rain with patches of fair and sunny.
No you cannot overlap weather, but if you use different regions next to each other at narrow canyons, paths, etc its barely noticeable in game the demarcation line between weather areas.
OR you can use triggers to change the weather.
Fountain: Instead of using the default fountain of life and mana units, make a custom one using the ruins fountain model, that would fit more in the landscape than the fountain you have. There are two fountains, a round one and a 'wall' one this may give you more options when it comes to fountain units.
Or the cityscape fountain, there are various other doodads you can use as replacement models for various purposes.
Lastly, great terrainers don't just happen, they reach greatness through trial and error and by trying different things with their maps. You mayn't be good at it right now, but if you play with it, try different things and customize doodads and your tile set you most likely will become a great terrainer.
