It's only opaque if you don't care enough to study the question. Ursula von der Leyen was chosen by the members of the European Council.
The European Council, among other responsibilities, "decides on the EU's overall direction and political priorities", and "nominates and appoints candidates to certain high profile EU level roles, such as the ECB and the Commission". [1] If you have to know only one thing about the EU, it's that one: power lies in the hand of the European Council.
The current members of the European Council are: Alexander De Croo for Belgium, Boyko Borisov for Bulgaria, Andrej Babiš for the Czech Republic, Mette Frederiksen for Denmark, Angela Merkel for Germany, Jüri Ratas for Estonia, Micheál Martin for Ireland, Kyriakos Mitsotakis for Greece, Pedro Sánchez for Spain, Emmanuel Macron for France, Andrej Plenković for Croatia, Giuseppe Conte for Italy, Nicos Anastasiades for Cyprus, Krišjānis Kariņš for Latvia, Gitanas Nausėda for Lithuania, Xavier Bettel for Luxembourg, Viktor Orbán for Hungary, Robert Abela for Malta, Mark Rutte for the Netherlands, Sebastian Kurz for Austria, Mateusz Morawiecki for Poland, António Costa for Portugal, Klaus Iohannis for Romania, Janez Janša for Slovenia, Igor Matovič for the Slovak Republic, Sanna Marin for Finland, and finally Stefan Löfven for Sweden.
If you don't like the direction of the EU, ask your representant to do something about it. Otherwise pick another one. They are all democratically elected (directly, or indirectly in parliamentary systems).
[1] https://europa.eu/european-union/about-eu/institutions-bodie...