You over estimate or intentionally over represent the power of the EUP in the confirmation of the council, for the most part it's a formality. The power to nominate is by far more important than a approval.

As far the the legislation goes again you are mixing the various types of legislation codified within EU law, Regulations and Directives can only come from the council, Decisions and Recommendations can only come from the commission, Opinions like well the old saying says can be made by all 3 bodies. For the most part outside of mostly formal proceeding the EUP only issues opinions nothing more, Directives are the most common issue of EU law as they leave room for member state to decide how to "interpret" and implement them, the only really binding EU law is Regulations which can only be adopted by the Council the EUP doesn't get to vote on it.

You need to understand that for the most part no one gives a flying fuck about the EUP what matters is the council the council is the one that represents the Governments of each of the member states they are the ones that make the decisions. The EUP is full of people who are non-electable in state level politics and no serious politician actually wants to get involved with the EUP there's no glory, no power, and no money in play there.

You can continue arguing about semantics but you need to understand that there's much more to politics than de-jure agency if you look at every political system in the world you'll find that often the majority of the power tends to fall into the hands of positions and bodies that might not or should not have power at all on paper, the US politics are a great example for it.

As far as the EU goes the only thing that matters in terms of de-facto policy is what the Governments of the member states want no some yahoos that got elected in elections that no one really cares about with 40% or some times less turn out, and the treaties that the EU is based on leave gaping holes to ensure that member states keep their sovereignty and agency because outside of a very few or well actually one state with so far suicidal social and political tendencies most member states still value their sovereignty over unity and considering the Euro-skepticism within most state level political systems these days it is not going to change any time soon.

Have a nice day.

P.S.

ai16 Special legislative procedures

Special legislative procedures replace the former consultative, cooperation and assent procedures. The objective is to simplify the EU’s decision-making process by making it clearer and more effective. As their name indicates, these procedures derogate from the ordinary legislative procedure and therefore constitute exceptions.
In special legislative procedures, the Council of the EU is, in practice, the sole legislator. The European Parliament is simply associated with the procedure. Its role is thus limited to consultation or approval depending on the case.
Unlike the ordinary legislative procedure, the Treaty on the Functioning of the EU does not give a precise description of special legislative procedures. The rules of special legislative procedures are therefore defined on an ad hoc basis by the Articles of the Treaty on European Union and the Treaty on the Functioning of the EU that provide for their implementation.

And no there isn't much limit on the "special legislative procedure" for the most part the council can enact it at any point which is why even when the ordinary legislative procedure is used the role of the parliament is much more formal and official.

This is one of those many many loopholes I've talked about that pretty much allow the Governments of the member states to have full control over the union and not vice-versa.
If you still want to argue, well have a nice day again!