Every piece of the submission puzzle tells the agent what she needs to know about the writer. Yes, the ultimate goal for the agent is to find the next great novel -- it's always the novel itself that is the bottom line. However, who's got time to read every manuscript that comes their way?
A query letter tells the agent if the writer is serious about his craft. Can he even write a decent business letter that interests her? Does he sound professional and easy to work with (and not a pompous azz)? Does he have credentials? Does he know what he is selling?
The synopsis tells the agent if the writer even knows what his story is about. Can he summarize his major plot points and characters with clarity in an easy-to-follow format? Can he write succinctly, or does he rely too much on vague adjectives, adverbs and poor verbs? Do I know what I need to know about the entire story arc, or am I left with even more questions?
The partial (3 chapters, 50 pages, whatever) tells the agent if the writer can indeed tell a story. Does he have a good writing style? Is his grammar good? Can he begin a novel? Is his prose any good? Am I turning the pages even though I have ten million other things to do and manuscripts to read? Do I want to find out what happens next when I'm done with the last page?
As writers, we can't trivialize any part of this process. If we want to get published, we need to learn and master these steps.