Use clear segues into adjacent points in your paper. Your essay should flow well, rather than stopping and starting in a blunt fashion. Make sure that each of your body paragraphs flows nicely into the one after it.
Annotating your research can take quite a bit of time, but needs to be taken one step further in order to add a bit more clarity for the outlining process. Organize your notes by collecting all of your highlighted phrases and ideas into categories based on topic. For example, if you are writing a paper analyzing a famous work of literature, you could organize your research into a list of notes on the characters, a list of references to certain points in the plot, a list of symbols the author presents, et cetera.
An easy way to develop your thesis is to make it into a question that your essay will answer. What is the primary question or hypothesis that you are going to go about proving in your paper? For example, your thesis question might be “how does cultural acceptance change the success of treatment for mental illness?” This can then determine what your thesis is - whatever your answer to the question is, is your thesis statement.
If you are writing a research paper for a class, consider the other students. Is it likely that they will also be writing about your topic? How can you keep your paper unique and interesting if everyone is writing about the same thing?