The EU Parliament doesn't have equal legislative power. EU Commission proposes legislation, and the parliament can only accept or reject. Of course informally they can discuss with the Commission and let the Commission know what they would or would not pass.
> effectively representing the citizens while the Council represents the member states governments
This is true. But you maybe forgot another body, the EU Commission.
EU Council, Council of the EU: Represent member states
EU Commission: Represents the EU
EU Parliament: Represents the citizens
I guess US doesn't have a body like the EU Commission, that is not elected and that represents the interests of the "deep state".