Not leaving enough work for night shift is not a criticism of inefficiency. It's the dominatrix verbally punishing the (insert official term, which I realize I don't know.) Giving it a low rating is the joke. If anyone's the target here it's Seven for being unreasonable and the Doctor for being a stooge.
As to operations? Kim scanned until Astrometrics went on line, opened hailing channels and I think rerouted power a lot. Seems important to me.
Again, in context it seemed pretty clear that Kim wasn't a senior officer until after the Caretaker disaster. Janeway in Twisted expressed her pleasure at Kim's success in meeting his unexpected responsibilities so successful. Which implies some element of surprise after all.
Harry wasn't going to get the girl because he was there to make Tom look sexier by contrast. When he did get the girl in The Disease she was the only alien that the Universal Translator gave an accent to in the entire twentieth fourth century.
The failure in Timeless is a plot hole because Old Harry's plan would have come straight from the Star Fleet analysis of the original wreck. Which they are going to do because they'd like to have the drive working so they can use it. Old Harry's personal creative work was the on the spot calculation of a way to safely emerge. Which is in fact an impressive feat.
Nightingale is actually an attack on network suits micromanaging (whether the writers meant to include Berman?) The story does absolutely depend on Janeway, Chakotay and Tuvok not bothering to check out the aliens' story about a medical mission, which is also incompetent. And it turns on Seven of Nine being a total master of human relations even while simultaneously showing all the tact of the Collective.