Generally, "we're consulting you the citizen" or "have your say" projects are just part of lookgood PR, and no one in a position of influence takes the opinions expressed seriously.

If the EU really does want to involve citizens more, then I fear they need to up their game considerably. It's not only that the Your Voice site needs finding and requires some Web knowledge to get around, it's also that it's not bang-smack updated and there are broken links (I found others than those you point out), which suggests they're not really putting the means behind it.

Also, at the very least, they should prominently explain who or what is a stakeholder, and why such or such a consultation is limited to stakeholders, or what the decision process is on that question; and they should be challenged to open as many consultations to the public as possible.