I have spent a significant amount of time in the last few weeks analysing consultation responses. As you analyse, it becomes quite clear what makes a good response, so I thought it might be useful if I set down my thoughts. My starting point is to assume that writers of consultation responses are aiming to maximise the likelihood of their view point being influential. With this in mind, here are my suggestions.
Keep it short. Using the minimum amount of text to get your point across makes it easier for the analyst, and also ensures that the correct point is registered. Brevity leads to clarity. If you have evidence or data to support your points mention them briefly, but provide a link to a place where the full information can be found.
Answer the question. A lot of thought goes into the questions that are asked in a consultation and they reflect the information that is required. There is no need to provide general background, or reflect back points made in the narrative elements of the consultation document itself. Only answers to the questions are needed and the other material just makes it harder for the analyst to spot the key points. If you really feel the need to make other points, there is often a catch-all 'any further comments' question that has been put there just for this eventuality. If you have nothing to say in response to a question, that's fine, just leave it blank.
On a related point, I would also recommend that you use the structure provided by the consultation framework, rather than put in a narrative response that uses a different structure. This just makes it harder for analysts to properly take into account your points, and risks that they will be misinterpreted or missed altogether.
Make your answers self-contained. In my experience consultations are almost always analysed by more than one person, and the logical way to divide the work up is by question, not by respondent. In this scenario, 'see my answer to Question 3 above' is not helpful. If you are answering the questions as asked you shouldn't really need to do this anyway, but if you do want to include the same information in response to more than one question, just replicate the text.
Don't challenge policy decisions that predate the consultation. This is linked to point about answering the questions. A consultation response is not an effective place to challenge the assumptions that underpin the consultation. If, for example, the consultation is about how to implement a good bus service, the response is not the place to argue that a train service would be a better option. Of course, there is no reason not to challenge policy decisions that have already been made, but the focus of the consultation is on the issues that are still open for decision. Trying to use a consultation response to challenge assumptions won't work, and your effort would be better expended on other approaches.