Contrary to some of your opinions, I thought that its frequent switching from dark to sex jokes to comedy and then back to the action again was really nice. In the first place, I didn't expect a continuously darkening atmosphere for the visual novel because of the prologue shown to us at the start of the visual novel. I do think that most of those jokes are in line with the characters' personalities, and have no effect whatsoever on how things go by. Why, those jokes are important in reinforcing the idea that Haru seldom falters in front of impending doom that they frequently face. I thought it was a nice touch. Most of these 'dark themes' recur inside the minds of the characters anyway. It is, in a way, a method of making the characters appear stronger than they should be, given how they're acting in a specific situation.
Also, I enjoyed Mayuki's route a lot. Sure, it didn't contribute much to the overall plot, but each route is a separate story anyway. They each have their own plots. Mayuki's and Ayaya's are prime examples of plots where Akihito wasn't dragged into whatever major's happening in the Comyunet. In a way, he was able to retain his 'everyday life' by a certain degree, oblivious to the fact that there are uprisings happening in the city. He played no major part in the fight for power, giving whatever plot those two routes had a 'sense of calmness and everyday life'. You could also notice that you barely see Caesar's Legion and the Round Table in those routes.