The daughters of Aku were a really great idea that was handled exceptionally well. At the start.
Having the daughters stand in Jack's way to finishing his quest was a way to raise the stakes. It could have been a perfect way to meet the mature expectations of a now adult fanbase. With a few rare exceptions, Jack was pretty much unstoppable in combat against robots and aliens and spirits. But when he has to face a fellow human, his own moral views as a noble and truly just Samurai and the entire point to his character are challenged, and in the end, he would have had to sacrifice some part of himself to fulfill his purpose in life.
If that were the main focus of the entire 10-episode season, if the theme of the show stayed consistent with the message it was trying to send, it could have been a slam dunk.
But I feel that he focused on too much, and in effect there was nothing in focus at all. Everything just kind of splattered together haphazardly in an arbitrary need to address every single thing. The three Gods, the Scotsman, the Guardian, some awkward shoehorned romance with a Mary Sue, all of the past people he's saved, etc. etc. etc.
Which I don't mind! But when you're only given 10 episodes to work with to finish off a massive epic saga, you better know what you're doing and pace accordingly, or it can (and did) end up feeling rushed.
So in the end, we got a series that, instead of having a tight focus and a few questions answered very well, we got a broad, shallow focus on everything and were given mediocre, rushed explanations.
With all due respect to Genndy, he's done some remarkable work, a romance is not at all fitting in Samurai Jack. I guess he just loves pale girls with short black hair too much and it leaked into this show.