There's democratic deficit in the whole system as this issue wasn't part of most internal election campaigns, effectively circumventing democratic process, due to lack of input from citizens themselves.
EU severely lacks checks and balances if it tries to be something more than trade union.
The EC has no democratic control, their members are not elected, only the commissioners are "approved" by the european parliament. Its actions are also obfuscated and mostly non-public (as we saw in the ChatControl case, for instance), so citizens hardly even know what's happening.
The president is responsible for the secretaries of State actions, and more generally their respective parties.
No one is responsible for the commissioners' actions, and they can't be fired. When Von der Leyen lied and refused to show her text messages where she privately negotiated Covid vaccines, nothing happened. When the EU commissioner for digital markets left and got hired by Uber right after... nothing happened, as no one was responsible.
Commissioners hold the legislative power, as they choose which laws to introduce and hold the pen during negociations. It's pure, unchecked bureaucratic power that ends up with a never ending flow of stupid regulations that weaken Europe slowly.
I'm suggesting that there are enough layers of interdiction, that you can easily 'wash' political fallout and push legislation that would otherwise get you voted out of office in local elections.
EU severely lacks checks and balances if it tries to be something more than trade union.