The problem is the indirection. Only the European Commission can propose legislation [1], so the legislative direction of the EU is entirely determined by them - MEPs can only slow it down.

And citizens don't vote for the Commission directly, meaning there's a lot of backroom dealing in its selection.

[1] Which also covers, I think, the act of repealing prior legislation.

True, but this is the same as with most EU countries government. In France, I can contact my Ministers... but to what avail!