how does the normal citizen vote for the president of the European Commission? How do we vote them out if we dont like their governance anymore?
As is the case with the chief executive in most parliamentary systems, by voting for an MP (in the case, MEP) of the party which backs their preferred (or opposes their opposed) candidate for leader.
But since you asked look at how little power a British MP has to get a private member's bill through to a vote. In actual fact the only private member's bills that get a vote let alone pass are those with government support.
Also the House of Common's isn't really democratic in any meaningful sense of the word. It took 886,400 votes to get 1 Green MP but only 25,900 votes per SNP MP. Similarly 38,300 per Conservative MP to 336,000 per LibDem MP. That's an order of magnitude difference between votes to power.