That almost nobody voted in the election, that nobody knew who the leader - or the platform - was going to be, and that she was absolutely chosen after the fact, by unelected leaders, that she cannot be sanctioned or replaced, and that elected MEPs cannot propose legislation - is fundamental to the nature of democracy.
Even in proper democracies, particularly in Parliamentary systems, even the budget requires approval without which the government falls and elections are called. Why? Because the proposition of budgets necessitate popular sanction. Parliament - and even legislative assemblies can dissolve government if necessary.
Ursula von der Leyen has unambiguously the least democratic legitimacy of any leader in the free world, by far.
The fact that the EU was purposefully designed this way - in the very face of very healthy democratic institutions i.e. Switzerland, UK, Germany - implies the lack of democracy was very much 'by design'.
It's an existential issue.
People usually vote for parties and the persons within them, not an individual.
But - the party, platforms, PM etc are very transparent, and elections are held on that basis.
If the Conservative Party of the UK ran with B. Johnson and Brexit, but then after the election decided to make some randome guy from Scotland - that nobody ever heard of - the Prime Minister, and said Scot made a 'Throne Speech' with some completely different agenda ...
...there would be a revoluion.
And of course PM has to be someone elected at their riding for good reason.
It's simply not good enough to say 'someone voted somewhere' so therefore 'it's democracy and we can do what we want'.
Consider Socialist Yugoslavia, the main difference between its electoral system and those of non-communist states was the amount of indirection involved.
Also, you ignored the second half of jariel's comment.
What you are complaining about is that she was elected by newly elected representatives, but not directly elected by citizens. I find this to be hairsplitting and meaningless in a context of representative democracy.