The EU, like most union governments including the USA, was designed to be conservative and not pass things by default. For something to pass the EU, it has to be wanted by both the leaders of all the EU countries (the commission) and the people in all the countries (the parliament). It's similar to the house and senate of the USA
You are misunderstanding the leadership structure of the EU. There are three main bodies that lead it - the Council of the European Union, the European Commission, and the European Parliament.
The Council is the one that generally consists of the leaders of each member state. It has important roles in the system including selecting candidates for key roles and as part of "trilogue" negotiations (which are themselves sometimes controversial for being secretive and unaccountable) but has little formal participation in the normal legislative process.
The Parliament is the one whose members are elected by the citizens of the EU. Its best known role is to debate and vote on new legislation.
The Commission holds much of the real power as it serves as both the leadership of the executive branch and the origin of new legislative proposals - and yet its members are chosen via much less transparent means and have little personal accountability to EU citizens.
Many EU commissioners have been politicians whose national political careers were struggling and - like appointment to the House of Lords here in the UK - they may have been put forward for the Commission by their national political leadership as a position of influence that required less confirmation than winning a popular vote. This is relevant here because von der Leyen herself is arguably in this category.
