Late response as i rarely check HN replies.
European Commission is so disjoined from electorate through many layers of elections, that it can disregard it completely - practically citizens have no input on EC's body. Any legislation originates from there which makes it even worse.
Only guarantee of EC doing their job is their Oath, and vote of no confidence is basically impossible to call, nor there's a way to initiate one from citizens side via for example a referendum. There are no consequences for not following the Oath at all so corrupt EC can easily push things that are favorable for bigger voting blocks, while screwing everyone else and get away with it.
The only measure that citizens have to actually affect EU turned out to be worthless(as SKG initiative has shown) - as Citizens Initiative is not binding at all, and can be disregarded.
EU itself creates a system of double loyalty for every politician - do they pursue national interest or do they jump ship to European ones(including appointed positions)? This erodes national systems of check and balances.
European initiatives are impossible to control nor audit form member state PoV, and it's even worse from citizen PoV. And there's no mechanism to counteract bureaucratic bloat growth, nor rampant lobbying.
European Council is used as a way to launder unpopular legislations and push it onto all member states - like chat control.
Most of the times none of those legislations have been a part of internal political campaigns - and even if they were, they were such in only single member state. There was zero input from citizens, even in forms of voting for their own government.
President of European Parliament can act against parliament itself, again with no mechanism for any consequences(ie best example is pushing chat control vote just before summer vacation this year)
Whole institution of EU after Lisbon Treaty was made with assumption that every member state will pursue their own best interests, MEPs will pursue their own best national interests too. But sadly this created system in which it is difficult to purge any form of corruption(both embezzlement/criminal, pursuing personal interests or being purely ideologically driven without consideration of practicality).
This was done to create resistance to populism, but in practice created system that's extremely resistant to purging corruption.
It doesn't help that EU itself is a very top-down organization. Not in form of dictatorship - it's far from that - but in form of committee driven changes by unelected civil servants that operate like a black box.
and one last thing, not related to checks and balances - EU itself moves at glacial pace and is resistant to change by design - which would be perfectly fine for just a Trade Union. Unfortunately it leads to it both not reacting in time, and pushing initiatives that are already outdated.