Well this is comming along nicely!
Couple of things (from my ever so limited viewpoint).
I preferred the land without the drop shadow. It now appears to float above the water. I've always liked to make my shorelines a dark sharp stroke with a light blurry stroke outside that - more like a light outer-glow.
The water might look "off" to your eye because it is in a very different style from the land. The land is very lush and textured, the sea is smooth and boring. I might suggest one of a few things to try: If you have a terrain (height field) map for the sea as well, use that with a light blue to dark blue map. This would give it more texture that would show how the sea floor features follow from the land features (kind of like google-earth from a high elevation). Alternately, limit the gradient to two colours - a lighter one for the costal shelves, and a darker one for everything else, then apply a light texture over the entire surface, something that is suggestive of water/ripples/waves noise.
For the borders, choose semi-transparent, hard edged strokes using colours not found in the natural world. Also the choice of brown is probably not good for a road as it blends in too much. The other option is black dashed on a light stroke like I used in my Niagara map (June contest entry). This will really jump out.
If your map is that large (wow) you might want to actually scale the map and redo some of those border/city/road indications on a smaller map to show the information "globally" This has always been an issue. (Or make the whole thing SVG and have the text scale dynamically (...but I digress).
More alternatives to try:
To make features pop, try using a complimentary colour. So as your dominant background colour is green on the land, red will stand out against it. You could use a browny/red which will pop less, but still give you a brown. For extra pop you could use a glow or a drop shadow, but that may be too much.
Like RobA said, the drop shadow on the coastline makes the map look a lot more cartoony - but I like it. I guess I like cartoony
I've always liked simple sea colours so attention is drawn to the land (if that's where you want it to be drawn), although again, as RobA says, it may look inconsistent.
It's a lovely looking map. Can't wait to see what you come up with next.
I found this thread searching for something else, and figured I'd ask and see if there are any updates....