I think that's kinda of contradictory. To me it's indeed pretty simple, if you want a game where every girl is in the harem, you simply can't have deeper "classical" romance (like in Eve's case), somewhat meaningful male friendsships (like Erik or Harold), etc. without it becoming totally weird or totally out of character.
I get that people don't care for these things and would be happy for DC to ignore it, but I simply think that this whole "full harem" thing just doesn't fit SS. There are games where the harem is key and where the game is essentially tailored/written towards it and quite a few of them are great. But SS wasn't meant to be that way and it shows in almost every story.
I strongly disagree here, to be honest. For the simply reason that it basically never works. Once you have to start "bending" existing stories they either become bad or boring or seem really lazy.
Also I don't really want to see that content wise, either. I'd like to see Harold and Helen back happy together while MC is having fun with Mia and Yumi. I'd like MC and Judith to kick some Latina ass without having to think about that MC has to fuck them later on, I may even like to get rid of Mrs. Smith for good if that that's an option and have MC take over her cult, etc.
If everyboy has to stay on "good terms" and be available for the harem, it just cuts off so many possibilities which in my opinon would be quite sad, given the great options the game offers.
Just do add: I'm not saying there shouldn't be threesomes, foursomes, fivesomes, whatever else is possible - but just that it should be within character and fitting for these specific stories. Even now the game offers more realisitc possibilities than DC could ever complete and to me that's really enough.