Something maybe to the effect of "As EU citizens concerned with Energy issues and having participated in other effective EU consultancies we wanted to bring to your attention some serious flaws in your consultancy process which may affect your ability to make inferences from the feedback you receive. We take the time to bring these to your attention in the hopes that changes can be made to improve the current process."

Some readers will only read the first paragraph and you want them to leave with an understanding of what the key issue is or be enticed to read on.

It seems to me the letter is making one main point:
The consultancy process is not credible because the questionnaire is so restrictive and problematic and cannot be interpreted as a legitimate public opinion poll.

To which I think rg's "how to do it better" question is answered by pointing to the fact that other EU bodies have had credible consultancies so it is possible to do so.

One last comment - it may be helpful to include in the letter the web link to the consultancy questionnaire & maybe even the Biofuels consultancy web site we mention as a "better/best practice" example.

Feel free to ignore or use as needed.