Personally I would love to see this game divert from what was written in the comics such as allowing the Player (and Haru by extension) to explore this world more in depth. This world has so many different characters already and plot points that I feel were either dropped or not fully explored when you were doing the comic (especially in the earlier chapters) that now could be expanded upon in the game. A few examples include following Miss Akira Tachibana into her storyline (aka Teachers Pet) however with Haru being able to get caught up in her little games possibly with Haru becoming one her pets in the process or having more interactions with Yuuki at the gym. Another thing I would love to see is an option to pursue Kagura as a love interest or possibly working things out to where either Haru or Kagura becomes Miyuki's sub while the other marries her instead (bonus points if Miyuki puts Kagura in a chastity belt to keep her urges in check before marring her) as alternate endings. Alternatively having a story path where Miyuki embraces her Dominant side and takes more control of her relationship with Haru could also be interesting to explore.
Now that I got my ideas and feelings out of the way here are my answers your questions
1) Would you prefer deeper relationships with a smaller cast or more characters with shorter optional storylines?
The cast that you have already built in the comics is already rather large so adding more would only increase the workload of game development so bare this in mind, that said having other romance and relationship routes would be a nice addition to the story and would be a good way to expand on existing characters plots and flesh them. Ultimately I have nothing against expanding the cast so if you feel comfortable in doing so then by all means, just don't go overboard.
2) Would you enjoy more gameplay mechanics, or would you rather keep things simple and focus primarily on story content?
Honestly this all depends on you, if you want to make the game have skill based outcomes that effect plot points go for it but personally that also mean you need to make sure that all of the possible outcomes are meaningful to the player, same goes with jobs there needs to be a reason for the player to need to do them and something to spend that hard earned cash on.
3) Are there any other websites or phone apps you'd like to see?
The only other website I think you should include is a porn site, lets be honest any boy in collage is going to need to relieve themselves and a site that helps them to do so is a must not to mention it would help them explore their budding interests as the story develops and could give opportunities for other people to take a peep into what turns player's version of Haru on allowing them to peek into Haru's mind (could possibly effect how the story progresses).
4) What locations would you particularly like to explore?
Not so much of a "location" but as I already mentioned being able to explore storylines from other comics like Teachers Pet could be interesting, admittedly these stories may need to be reworked to make them fit so not all of them might be possible.
5) Would you prefer longer, more detailed scenes or a greater number of shorter events?
Honestly both would be nice, more sexy scenes in general would be my choice, the length of the scene doesn't really matter much to me so long as they are enjoyable and interesting. Personally I would love to see more detailed scenes about Haru coming to terms with being in a cage, more teasing/edging/denial scenes, and more scenes with BDSM, Dom/sub interactions, and bondage all would be nice.
6) Is there anything currently frustrating, confusing, or unnecessarily repetitive?
So this is just my own opinion but why do a game based on My Roommate is a Futanari? I kind of understand the idea behind it but the reason I am asking this question is because based on everything you have asked in this questioner and said in the devlog it sounds like you want to build a sandbox game based in that universe (which I really like btw), however trying to make a game that tries to follow the comic chapter by chapter at the same time confuses me especially if you intend to follow the same story. Now I am not trying to discourage you as again I love this idea but would it not be easier to reuse the major plot points, characters, and locations but change everything else so as to allow for the player to experience the wider world of the game/universe without being restricted by the plot of My Roommate or is that what you already have planned for the game?
