It was a pity that Charles Michel missed the opportunity to offer his seat to her for at least part of the meeting, especially when matters under the primary purview of the Commission were being discussed.

Michel showed, at a minimum, a serious lack of judgement. According to Brussels bubble journalists, this two-tiered seating was indeed mostly a casualty of the Michel-VDL rivalry: the EU Delegation in Turkey was supposed to be the main point of contact to arrange the meeting, but the Council (Michel's team) "sent an advanced team including a Protocol officer who established a direct contact with the Turkish Protocol thus complicating effective communication and coordination with the Turkish side."

Then, Michel didn't realized the exceedingly bad optics of seating alone with Erdogan while forcing his rival to a remote sofa, until it was way too late.

The Turkish side, who is blaming the EU protocol rules for the blunder, is not entirely blameless: Erdogan had already been seated with both the EUCO and the EC presidents, and there were three chairs; of course, both presidents were male at the time. The Erdogan team, who apparently are trying to appease the EU-Turkey relations rather than pulling a deliberate humiliation, didn't see the bad optics either - neither the bad optics of pulling out of the Istanbul Convention a few days ago. They may be furious at what they surely perceive as unfounded accusations, but they failed as much as Michel to see a problem with the seating arrangement.

Still, the main issue is, as you pointed out, is the rather weak and too often ineffective EU Executive. Unfortunately, this is by design: the head of states & governments in the Council have always wanted to have primacy over a possibly too active Commission (and over the EP, goes without saying). For the Council members, Michel, a former Belgian PM, is "one of us", and he is always insisting on his primacy, protocol or otherwise, over the EC President, until of course he overplayed his hand in Ankara. VDL herself was nominated to the EC after a not so glorious political career in Germany and has willingly played second fiddle to the EUCO.

Eventual change is not going to come from inside the EU institutions: only the EU governments can change, and eventually reinforce, the EU institutions. With the rise of nationalists, if not outright fascist, parties all over the continent, and the msinstream right parties jealous of their national prerogatives, it doesn't look like change is going to happen anytime soon.