A United States of Europe? Good Luck

W.r.t. the Commonwealth, even then the Commonwealth fell apart for three major reasons, viz., the so-called Swedish Deluge, the Khmelnytsky Uprising and the abuse of the liberal political system by the nobility with foreign meddling playing a major role. The second was ethno-religious in nature and the third driven in part by conflicting interests. (Indeed, the Polish Enlightenment differed from the Enlightenment in the West precisely because it dealt with the problem of too much or misallocated freedom.) The dispersion of military might among private armies (in some cases the sizes of private armies of wealthy magnates rivaled the royal armies in size) coupled with conflicting interests prevented the Commonwealth from being able to mount a coherent and unified defense against Russian, Prussian and Austrian dismemberment, and ultimately destruction, of the state. And while it lasted, even though the Commonwealth was a vastly freer place that permitted the peaceful coexistence of many different ethnic groups and religions, it nonetheless was held together by a dominant group with a dominant ethos, viz., the Polish nobility.

In other words, empires suffer from tension when they impose their will on the constituting nations, but they also suffer from a lack of coherent and unified interests among its members. The EU suffers from both.

On the one hand, you have the federalist impulse wishing to beat member states into submission by asserting a "soft" German dominance over the continent against the wishes of its members. On the other hand, you have the same politicians possessed by this impulse maintaining that they respect the individuality and alleged sovereignty of each state. We respect cultural differences, but we completely ignore them when gerrymandering policies. All members are equally important, but our policies favor the interests of certain members over others and have in place a voting system that privileges might over collaboration. The migrant crisis undermines the Schengen Zone. The Greek crisis undermines the euro zone. Nord Stream undermines the idea of common energy policy. The Ukrainian crisis undermines the idea of common foreign policy. It's easy to wallow in shallow sentiments in the absence of crises, but it is precisely during crises that the substance of such unions is revealed. The truth is that the EU is creeping dangerously toward a point of no return. Instead of serving as a platform for nations to find common ground and collaborate for mutual benefit, it has contributed to the opposite through its incompetence, its arrogance and its Brummagem unity concealing the real political interests at play.

The EU council and commission can issue directives, decisions and regulations without involving the EU parliament, the EUP is mostly for show it's opinions and recommendations are shafted there's a good reason why it looks like a circus filled with Neo-Nazi's/Fascists and Marxists (or at least that's how the extreme right and left like to call each other) with representation which is completely skewed from the geo-political reality within each member state.

The EUP still haven't degraded to the point of being a utter kangaroo court like the UNGC but it's not that far. If you think otherwise there's no point of continue to discuss it but if you follow EU politics you can easily see where the power lies and how and by whom pan-European policy is driven: hint it's not the greens, the pirates and the golden dawns in the EUP.

You're making a distinction without a difference (and you're muddying the waters between a proposal to appoint and the actual appointment; without the European Parliament, the European Council can only propose, not appoint). If the European Parliament says yes, the Commission is elected and can get to work. If the Parliament says no, it isn't and it can't do a thing. Same for how plenty of parliamentary democracies elect their head of government or cabinets. Lack of a write-in option does not make it not an election.

I note also that for all practical purposes, the "spitzenkandidat" system has factually replaced the power of nomination (not appointment).

> The EU council and commission can issue directives, decisions and regulations without involving the EU parliament

This is factually false, the codecision procedure (= what is now called the ordinary legislative procedure) applies to practically all legislative acts and requires the Parliament to vote for them. Legislative acts can include framework decisions with the legislature delegating implementing measures to the Commission (for example, the ecodesign directive, where the exact wattage for vacuum cleaners was then set by the Commission according to the guidelines of the directive), similar to how legislative acts in the US generally leave it to the administration to enact the necessary regulations. Note that even there, some implementation measures may be subject to parliamentary approval via the examination procedure.