Lucy not being upset over being fired from the AVL makes more sense for the reason she joined in the first place: Family. To explain, her reason for joining the organization in the first place was because a supervillain killed her parents, but in the present, she already has a family.
Valerie Da Vinci's Establishing Character Moment makes more sense when remembering Scarlett Overkill's complaint in the Minions movie that females in power have to work harder to be respected.
Lucy's difficulty with figuring out how to mother the girls makes even more sense, since not only is she coming in as a parent to them with little experience, but, considering that her parents were killed when she was young, it's very likely that she doesn't even remember what it was like to have a mother, and thus doesn't remember how one is supposed to behave.
Fridge Tearjerker: Robert never got a chance to meet his adorable granddaughters or Lucy before his death.
Dru going full villain in the ending may seem silly at first, but a bonus feature on the DVD states that the AVL now considers Dru to be their number one threat. Keep in mind that Balthazar Bratt, a supervillain crazy enough to almost destroy Hollywood, was the AVL's most wanted villain during these events. Dru has to have somehow done something just as bad or worse. Just what did Dru do to become the AVL's new most wanted villain?