First, let me repeat what I said in my page on effective communication:
Have you noticed how short my paragraphs are? This is intentional because of the medium. People reading on the Web tend to skim the material. They usually jump completely over long paragraphs.Written communication is difficult because you cannot see your audience. Nor do you know what they know. You must start by assuming complete ignorance and an inability to grasp your meaning... That's rough!
If I want to be read, I have to adjust my writing both to the medium and to the reader I am expecting. Take a look at TIME magazine. Their writing is a good example of clarity. They use small words, short sentences, and simple statements. They pioneered this approach. You should look at their work awhile and learn from them.
There are two critical elements to writing -- especially writing a research paper -- which many people skip. First is the outline. A good outline can summarize your thoughts and organize your writing and transfer of notes.
Second, and even more critical, is the element of REWRITING. You must repeatedly read over what you have written from the viewpoint of ignorance. You must re-write until your paper is simple, straightforward, easily understood.