Parliament rubber stamped the council nomination but where did the public vote for him?
Like in most parliamentary democracies, head of government is formally nominated by president or monarch (or European Council in case of EU), but it is the majority of the parliament who vote for him.
You have obviously forgotten that few in the EU wanted Juncker and if you think European politicians consider Junckers "election" legitimate then consider
Not really. Leading national politicians (e.g. European Council) did not want Juncker as EC president. After 2014 EP election there was conflict between them and newly elected MEPs whether the Council nominate Juncker or some of Council preferred candidate. But leaders of EP party groups expressed that they did not vote for any other candidate that winner of the EP election.
You think the public in Northern Europe would have considered the guy electable?
Well, definitely not worse than last five prime ministers in country me being citizen of.
My reading (and it has been some time) was simply that the commission can overrule parliament and that the council of ministers can overrule the commission.
From Wikipedia:
Article 294 TFEU outlines ordinary legislative procedure in the following manner. The Commission submits a legislative proposal to the Parliament and Council. At the first reading Parliament adopts its position. If the Council approves the Parliament's wording then the act is adopted. If not, it shall adopt its own position and pass it back to Parliament with explanations. The Commission also informs Parliament of its position on the matter. At the second reading, the act is adopted if Parliament approves the Council's text or fails to take a decision. The Parliament may reject the Council's text, leading to a failure of the law, or modify it and pass it back to the Council. The Commission gives its opinion once more. Where the Commission has rejected amendments in its opinion, the Council must act unanimously rather than by majority.
So EP can reject legislation in the second reading.
Rather than a simple majority vote we have an arbitrary 75%
Two-thirds is ~67 %, the usual margin for important decisions.
Well, after experience with unstable governments based on narrow majority of few MEPs, such hysteresis seems like a good idea even for national governments.