The point is that we have 2 levels of indirection before we get to the commissioners: national elections in EU usually determine the composition of the parlament, then parlament makes a government (first level). The head of government then appoints a commissioner (second level).
The decision citizens take at national elections is determined by a variety of factors, first of all at the national level.
Given this context, to claim that citizens have any influence on who's part of the EU commission is delusional. If they did, we certainly wouldn't have Von Der Leyen in power, since she enjoys a measly ~34% approval among EU citizens.
For example I think EU citizens are not able (as in not willing to put the time and effort) to understand and discuss what EU is and what kind of MPs we want there and what they can really do.
I even consider somehow that is a mistake to even vote for those if the discussion is not about the EU and the direction we want the EU to go but about how can we protect their own country where country = ANY of the members.
Hard to tell, to be honest. Maybe the solution is a presidential republic with a federal government like the USA. Maybe it's to give more control to the EU parlament.
IMO the EU has expanded too much for its weak government model, and has now too many conflicting interests within it. It can't work without a strong central government, and since we can't find an agreement between all members on what that government should look like, we might as well split into multiple smaller unions where members interests converge.
> I even consider somehow that is a mistake to even vote for those if the discussion is not about the EU and the direction we want the EU to go but about how can we protect their own country where country = ANY of the members.
I agree, that's why it doesn't make sense to go through national elections to pick a commissioner, that will also skew the vote in nationalist terms. We have the EU elections to take decisions about the EU, but it turns out the EU parlament is pretty much powerless.