A writer has problems establishing the mood of a piece. That's all on the illustrator. If you doubt that, track down some Johnny the Homicidal Maniac and then visualize the dialog as if it were being said by normal cute and furry animals. Or super-heroes. Or as part of a soap opera. The dialog still works, but the tone has changed; it has gone from being basically morbid to being fluffy, or serious, or even angsty. In order to establish mood, the writer has to be able to communicate that to the illustrator. To get a really good feel for this, track down the movie "Poison", where three entirely different film crews took on the same 30-minute script and came up with three entirely different movies.
The problem with communicating how the mood of the piece should be is the limits of the script format. The writer is limited to defining basic actions, dialog, and captions, and sometimes panel lay-out beyond the number of panels. If he's lucky, a writer can also define camera angles. That's a lot of information, but it provides little more than a skeleton on which the illustrator can hang any skin he wants, making it up to him to decide what the mood will be like.
I point this out because writers sometime forget how collaborative comics can be. When writing a script, it can be easy to forget that the way you are visualizing the script can be radically different than how an illustrator can visualize it. Not that it's necessarily a bad thing, just that the writer can really be put off when what was drawn is too different from what he wanted. There are some ways around this, but they all take actually talking to the illustrator in order to get the right mood across. This is why there are so many different meetings set up before a comic is really started; the entire crew has to be on board with whatever is going on.
Another way to do this is to set up a bible. A good comic bible comes in three parts. The first pat will be a description of the universe in general, along with any notes on physics, such as whether or not magic works and how, as well as important things to note, such as large organizations and a general history of the world. The second part should contain character descriptions and sketches, along with how they interact with the world and each other. The third section should be the continuity section, a brief history of the comic itself with notes on where the plot is going, acting as a road map for the action.
By setting up a bible, you can have a lot of input into how the world feels. Once you have set things up and things are going, you can have a lot of fun with the world. It is just a matter of setting things up right. And we all know how important those establishing shots when it comes to creating just the right mood.