Von der Leyen is the compromise between Macron and Merkel at the time.

Additionally, the general view is that politicians deemed incompetent in their countries are sent to the EU, where they could “do little damage”. The thing is with Von der Leyen, is that they gave her one of the most important positions in the EU despite the perceived poor track record of hers. I think you may be right that she was installed because favouritism also played part.