Answer: When writing, it is important to pay close attention to your usage of sentence structure, word choice, and the fluidity of your writing. Your writing should NOT be choppy or contextually confusing; one should be able to read your writing and, when beginning a new paragraph/main point/etc., be able to understand the transition that just took place. Although this entirely depends on how well you can write, paragraph/sentence-transitions are easier to pull off when writing a paper that has an introduction, where the main points and subject have been clearly laid out. However, transitions may seem choppy almost by default if your introduction (and thesis statement) are not concise and descriptive of what your writing is going to be about.
Lastly, try having someone you know to read it aloud or just read it back to yourself and if it sounds wrong then it may need some changing. (This is not recommended for perfectionists like myself)