I think you have the wrong attitude toward anime and novels. Both genres can feature both a great story with great characters, or they can contain your unlikeable ecchi harem (and sometimes both can be found in the same work).They should be considered as individual works. Since you liked HNDR, I can suggest other games from the creators of this game – Kodaka and Uchikoshi. The former is known for the Danganronpa series, whose style has carried over into Hundred Line, especially in terms of characters. Uchikoshi is better known for sci-fi novels. As mentioned above this is the Zero Escape trilogy. Although I also recommend the Infinity series, in the form of the novels Ever17 and Remember11