Rise above your data and write a logical account that not only sufficiently explains all concepts and steps, but that also keeps the relationship between these in view. Think of it as writing fiction with character development and a logical progression of the story.
Be open where procedures, options and thought processes are concerned. If you are aware of possible weak spots in your story, explain these instead of trying to hide them.
Pay close attention to the macrostructure. Make sure that loose components of your research connect well with each other and are described in a logical, flowing manner.
Align your writing with the operational base. The core of empirical research is the operational base. Not only the theory, method, result and discussion should agree with the operational base, but the writing style and interpretation must also align with this.
Consider the value of the review board's comments. Although you do not always hear what you would like, comments from the review board are in general--exceptions aside--constructive and contain useful recommendations for improving your article.
Give your article time to mature. Let colleagues read it; discuss and debate the bottlenecks; take the time to edit and rewrite and occasionally let it sit for a while so that you can pick it up again later for a fresh look.
This section is based on:
R. L. Daft, Why I recommend that your manuscript be rejected and what you can do about it, in: L.L. cummings and P.J. Frost, Publishing in the organizational sciences (1995, Sage Publications)