It's not easy to write a coherent plot. That's the POINT of written literature, of course (be it video games, movies, books etc.) because if it isn't logical then it doesn't matter what it is. It may as well be random events with no connection. It actually IS a string of random events if the plot doesn't have coherency. There is a technique in literature that is like this - the cut-up technique. The most famous example being William S. Burroughs' Naked Lunch. This technique is characterized by randomization of the plot elements. As in, no matter how you rearrange the parts of the "story" it has a logical plot. Though you have to realize that, by using this technique, you have to write the parts in such a way as for them to be self-contained and their chronological order doesn't matter. It's a bit more complicated than this as this is a rough outline, but it helps to illustrate the technique.
Back to D:OS - You can have comedic elements, but they must be set up from the start to avoid sudden mood shifts. D:OS does this. You also have to be careful not to switch genres in the middle of the plot. From a drama to parody, for example. Look at ME3's ending where the genre shifted in the last 5 minutes and it was incredibly bad and forced. It can be done if used carefully and sparsely. Shifting genres can be evocative, I like to use a movie example for this - Behind the Mask: The Rise of Leslie Vernon. It's a satirical mockumentary about a serial killer-in-training, but the second half shifts to full-on horror, it was done very well and thought-out. It showed how different a person that you know can be (oversimplification, but you get the idea). It had build-up and the shift didn't come out of nowhere. Another example is Audition, where it starts as a generic kooky asian rom-com, but turns very dark; it was also built-up very well. If the genre shift is *meaningful* and thought-out it's a brilliant move. This, coherency and the triviality of the characters is where D:OS suffers heavily. The plot (however disjointed and illogical it is) isn't moved by the characters, it's moved by Star Stones and Pandora's Boxes, gods and what-not. This placed the characters in the back-burner and it really doesn't matter who or what they are. The mood/genre also changes suddenly with no build-up and it's jarring, takes you out of immersion and breaks the 4th wall really badly. This isn't the problem of comedy, not really. Though serious violence, drama and killing aren't conducive to comedy, that is why most RPGs are "grimdark" and that is one of the reasons why D:OS is so absurd for many people. Look at South Park: The Stick of Truth for an example of how to make a comedy RPG. It is coherent in its genre from start to finish.
My point is, like I said, that it's not easy to write a coherent plot, because you stand on very complicated philosophical, artistic and intellectual concepts that are very hard to explain in a single thread post. They should try this in D:OS 2, though, no doubt about it. Even if it's a comedy RPG it should be continuous in its writing style, genre, characters and plot. Though they already said that it's going to be more serious. That doesn't change anything, it still should be coherent and thought-out in every aspect. The game being Co-op doesn't really have anything to do with this. It is strange how they interact with the rock, paper, scissors thing and it's just thrown in there for no discernible reason, and I think they should either rethink the approach or not have the main characters talking to each other like this. They can have predetermined dialogue, but that goes into different territory with the characters having a predefined personality. There is a lot more to be said on this subject, but I think this is enough for now.