The EU commission on the other hand actually has power.
As one other example, consider the Swedish terrorism law. There's no such thing as designating something a terrorist organization-- that's constitutionally impossible, instead it's determined by the courts. Meanwhile the EU commission can actually designate a group as a terrorist organization, no court case necessary.
>Ingen myndighet, inte heller riksdagen eller en kommuns beslutande organ, får bestämma hur en förvaltningsmyndighet i ett särskilt fall ska besluta i ett ärende som rör myndighetsutövning mot en enskild eller mot en kommun eller som rör tillämpningen av lag.
No authority [...] may decide how an administrative authority is to decide in a case involving use of authority against an individual[...]
Furthermore, the commission is not like a directors of an agency. They are politicians. I would compare them to government ministers, who are appointed in a similar way.
You seem to be under the impression that the executive branch in Sweden has no political rulemaking powers when it in fact has been given such according to constitution law.
The EU Commission does not make up rules anymore than these government agencies in Sweden does.