A few quick responses, I didn't have time to include a detailed explanation so heres some info;
Actually, water really is blue - it's not just reflecting the sky. So quite what colour large bodies of water on Mars would look like before the sky went blue I'm not sure - I doubt it would be very pretty though!
Yep, its the other way around, one of the reasons the earth's sky is blue because the sea is blue. The sea is blue beacuse of the other reasons that the sky is blue.

Certain frequencies of light are absorbed by the water (or water vapour) while others are reflected. In deep water red light is one of the first colours to be absorbed, so the seas on mars would likley be quite dark.
It looks very nice, although perhaps a bit on the dark side ... ?
The dark bits are desert and represent the black sands of the northern hemisphere. The lighter areas are sea, which in the early mod will represent aquafiers and frozen seas.
This all looks great. With the terrain, bear in mind that Mars is not overly cratered - it's not like the Moon. Most of the craters on Mars are on the higher land in the southern hemisphere.
Admitedly, the larger craters are in the southern half of the planet. However, if you get a realy hi res mosaic image of mars and zoom in on the north you will see that it is covered with lots of loose rocks and small craters. For the early scenarios I'm thinking of zooming in on a small area where this will be obvious. Later the cratered terrain will represent the southeren zone.
For now however I think that ther terrain will be;
Desert > sandy deserts, mostly black sand.
plains > Lightly cratered terrain.
Grassland > relativly smooth terrain.
Hills & mountains > Hopefully I can get these to look like two different height highlands.
Snow capped mountains > if the above works out ok these will be large craters or volcano mouths in the highland.
Swamp > shouldn't be too difficult to make these in to crazed canyons
Jungle > large craters
Forest > will probably use this to start with as rocky uplands to give the southeren highlands more veriaty.
Coast/sea/rivers > frozen surface water.
Last but not least the above images are slightly doctored, the edges have been blured and more craters ahve been added. Hopefully once I get all the Masks set up and saved ready to add the terrain.
This version, however, has no aftereffects, this is a raw capture from CIVedit.

This is the hardest parts of the first eras graphics done. Hopefully the add on terrain such as swamps jungles etc... should be fairly easy, just a matter of some BMP brush action. The hills/mountains etc... may be a little more difficult.