1. For the dungeon, remember we've got full-tile-type walls, so think about things like: one tile wide passages (player sprite needs to be able to fit in the corridor graphics. Pillars in rooms that are one tile big.
There are two ways to do this:
Floor tiles are absolute (minimum of 1 variation). Floor is visible around 16 permuations of wall tiles that will be used as wall near to floor, but are not navigable squares.
Wall tiles are absolute (minimum of 1 variation). Wall is visible around 16 permuations of floor tiles that will be used as floor near to walls, and are navigable squares, so need to accommodate sprites.
In other words, there are floor tiles and wall tiles, and they don't overlap. Am I correct? If so, that's not a problem - in fact, it makes things easier for me. What I could do is make wall tiles show bricks (or whatever) on only one side, and let your program trim the floors with wall tiles where the bricks show up aligned to the floor. Does this sound good?
2. I'd have personally favoured a slightly lower saturation than shown here, and perhaps with a slight colour wash to give a thematic colour tone to the game, or to different game areas, such as brown outside and purple in the dungeons. Perhaps different colours can be used for different dungeons? dark red, purple, blue and green washes are all possible tones.
We could always apply this to the tile set algorithmically during game initialisation.
Yeah, it wouldn't be too hard to take a grayscale or color tile and add a bit of color. Whether you guys do that though is up to you.
3. consider tile size for the dungeons. If dungeon rooms are 10x10 maximum, how much of the screen do we want the biggest room to take up?
The unwritten standard for 2D tiles is 32px * 32px, but these could be resized if you decide to use smaller. The only problem would be the steel mesh tiles, as the transparent parts would mush together and block the transparency.