You're describing the way a normal democratic government works. The EU parliament can't force the commission to do anything other than a mass resignation, which hasn't happened for decades. The "parliament" can't even propose changes to the law, let alone arbitrarily command the Commission like in a virtual government. That means it's not even really a Parliament!

I'm pointing out that your post is factually wrong. Now I'm moving on

You're using a (hopefully not deliberately) very deceptive set of phrasings to make it sounds like the EP or even the Council is in charge. Almost nobody tries to make that argument because it's clearly not the case and that situation is written into the treaties. All this stuff starts and ends with the Commission which is where all the actual decisions get made, the not-really-a-"Parliament" is just along for the ride and asked to rubber-stamp things from time to time. As for the council, it also cannot actually propose changes to EU law. He who makes the law ... makes the law, it's as simple as that.