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The commission has a range of powers that the parliament doesn’t have - the ability to initiate legislation and set budgets for instance. Yes, it depends on the parliament to approve stuff, but so? Like in the UK, which is the more powerful body - parliament or the lords? Obvs parliament, even tho it’s dependent on the lords to ratify its shit. Just because there’s some constitutional checks and balances doesn’t mean that power can’t lie more in one place than another.
Also, the commission gets up to a bunch of extra-curricular shit. Going back to Greece, it wasn’t the EU parliament in the troika, it was the commission. That’s an expression of power.
You’re confusing the council and the commission. The council is the elected heads of state (like I say, concentrated executive power). The commission is unelected. Both bodies are massively more powerful than the parliament, which is the only directly elected entity. This imbalance has been apparent to everyone for decades, but the EU hasn’t seen fit to reform.