As I have said in the past, querying editors and agents is very similar to looking for a job.
- Cover letter = Query letter
- Resume = Manuscript
- Pitch = Initial interview
I do have to stress that agents and editors are not out to "find reasons to reject an author or project. The reality is that authors really do this to themselves. Sloppy projects, rushed query letters, no focus in the query.... You get the idea.
While you might have your story finished, you need to really take the time that everything is in place and representing exactly who you are and what the story is.
One thing to remember is the combination of the number of submissions and agent or editor receives as well as the time they have available to read your project. This is why all of the agents out there have spent so much time on their blogs talking about what makes a great query letter and what falls apart. There isn't one right or wrong way of doing a query, but there are things you can do to enhance the quality of your project. Take the time to really look at what you send.