The trouble is that none of the parties involved have any incentive to fix this. The national governments certainly don't, because it gives them a convenient way to pass laws they don't like, and the EU doesn't either because it both gives the EU more power and makes national governments beholden to them. For all the talk some populist politicians make about leaving the EU, it's not like they actually would because that would mean giving up their power to pass laws without that inconvenient democratic accountability.

I reckon this was a major reason Brexit went the way it did. Supporters of the EU liked to point to the fact that actually, our government was behind a lot of the unpopular EU actions to argue that Brexit supporters had been tricked into wanting to leave the EU. What they didn't get was how completely unconvincing an argument that is. The politicians who were busy undermining and blocking any attempt to leave the EU also used it as a way to pass laws that the people they represent didn't want, shielding themselves from any kind of accountability to the general populace, and that was meant to make everyone fall in line behind them and want to remain in the EU? Ridiculous.