My problem is the lack of democracy through the too-indirect way that the commission is elected. Von der Leyen was an extremely unpopular and horribly incompetent (at least in charge of defense) minister in Germany, then somehow she became president of the EU commission. Her skill seems to be politicking with other politicians. That would not have gotten her elected in an election by the people.
Sometimes its a good thing that people do not elect directly. They participate indirectly though. And there are general rules to follow. So its more stable framework than full public control each election cycle, because the populism happens and if you want to be elected you cant take unpopular decisions which sometimes are needed.
Indirect democracy is not really a lack of democracy. But I dislike the way it works now as well and would like for EU elections to be more direct. I'd also like to be able to vote for candidates from other member states.
However changes like these are deeply unpopular as they get interpreted as moving more powers to "Brussels" by right wing media.
And it is the nation states that fight tooth and nails against more direct elections.