You're promoting a logical fallacy, one that insists a transnational commission is the direct equivalent to a sovereign parliament. The British government can be overthrown every four years in its entirety, sometimes sooner. There is no opportunity for an EU equivalent. With very few exception EU representatives are pro EU, they perpetuate the union they serve. There is no party structure offering differing opinions on its role.
There are very few members of any parliaments that support the dissolution of said parliament - the SNP and Plaid Cymru being the obvious exceptions in Westminster (making up just 9% of the seats in the Commons). This is probably quite high by most standards - I doubt any members of the United States congress or senate support dissolution of their Union. By contrast, the European Parliament has 208* members who are signed up to Eurosceptic political groups (27% of MEPs). The European Parliament is actually, on the whole, pretty sceptical of itself, and I'd hardly say that 208 members could be considered "few exceptions".
The fact that most members of any parliament support the existence of that parliament is no surprise. This is in no small part because most people who go into politics do so to advance their causes, and they usually do so within the parliamentary system. Those who don't want the system to exist often wouldn't want to serve in the parliament that they would dissolve. There's often also a sense of apathy amongst voters who don't want the EU to exist - they see no point in sending members to the EU so they were perhaps underrepresented in the EU elections.
But I'm sure you're about to point out that Westminster is a national parliament whereas the EU is something different. I'd agree that the EU is not a national parliament, but I'd disagree that it functions in a different way as a result of that. The parliament is subject to democratic processes. We vote(d) every five years for our MEPs, as does everyone else in Europe. As such the parliament is dissolved every five years and we have another opportunity to vote. We can change the makeup of the parliament, who can in turn initiate a vote of no confidence in the commission. This is exactly the same as in the UK.
You are the one who seems to be committing the logical fallacy here, in that you seem to assume that the EU is a political party. It is not. It is a system of government like any other, and as I've said there is the opportunity to "overthrow" the government, as you put it. It relies on us voting in candidates to enact that change. Sadly, most of our recent elections here in the UK have focussed on our continuing membership of the Union rather than our actions within it.
*
MEPs who are aligned to any group of parliament that describes itself as "Eurosceptic".
