How badly would you say the council or commission have to mess things up before they saw any voter-initiated repercussions what so ever with a system of accountability that requires voters to consider punishing the council or comission more important than their own national elections?
If accountability is to work, it has to be more than an abstract theoretical possibility.
It isn't abstract. Your government sends representatives to represent its platform and priorities. If you don't agree with the reps you need to elect a different government.
It's a abstract because you will never ever see a situation where voters neglect national elections to adjust the EU council or commission. Maybe it's what needs to happen, but the way thing are arranged it just won't.
Why "neglect"? You're voting for a government that does the things you want.