You're missing the point. And factually wrong on some things.
First off, international comparisons cut no ice in the United States. Right or wrong, our legal and political system cares not at all how things are done in other countries. How the EU runs its elections would have zero influence in the debate here. As many forum discussions here have shown, many Americans aren't even aware voting systems besides FPTP exist.
The Electoral College and the Senate *both* exist to give the states representation independent of the one-man-one-vote principle. When we vote for president, we really hold 51 elections, and each of those elections gives the winner of each a certain amount of votes in the Electoral College. How many electors each state gets is only indirectly tied to its population.
If we abolish the college, we take states out of their central role in the process and, implicitly, make them less than the legitimate, popular polities they are now. We would be making this radical change due to a desire for a more openly democratic method of election and representation. So how can we continue to justify a chamber of Congress where the half million people in Wyoming get two senators and the forty million people of California also only get two?
We can't. If the Electoral College is an intolerably undemocratic institution then the Senate is grossly more so. This obvious problem would make Senate reform irresistible. And since Senate reform is very hard to do and many vested interests would be upset, the Electoral College will not be abolished because those vested interests will head the problems off at the pass.
As for you being factually wrong, the EU parliament is not elected by regions everywhere. Member states decide how the MEPs are elected. Most just use a national proportional system. The Commission is appointed by the European Council, made up of member states' heads of government, not just any old ministers. Unless you're referring to the Council of the European Union, a separate body which is comprised of member state governments and has a role in lawmaking.
At any rate, any EU comparison is inept because the United States is not a supranational entity.