Good read. Not much to add myself since this is more or less the same thoughts I had when it comes to relationships and choices in games, my particular examples being The Walking Dead series and Fallout. Somebody already mentioned it earlier but Persona 3 had your (female) social links revert to a "Broken" status whenever you engaged in social links with other girls, though oddly enough you can get around the system by maxing the links one at a time. Even if it was broken you can be easily fixed.
Persona 4 kind of got around this system by letting you decide whether you wanted a romantic relationship with the girl but it was a bit useless (in terms of a game) by the fact that the "Broken" status was removed, although technically speaking it's still there albeit only in the Naoto route for different reasons. In a way I wish they kept the system or designed some other way (though Golden does acknowledge the multiple relationships at certain events.) It's highly unlikely it'll ever have it but I've always thought the concept of a polyamory relationship would be interesting to have (assuming that everyone involved is 100% honest with each other, if not it can always be a catalyst for drama as they are want to be.)
As you mentioned however, the realities of game development mean that having so many different permutations is a messy and difficult business to handle properly. Fallout handles it via the image montage with a voice over which does work even though it does feel rather sterile and a bit "gamey" while the Walking Dead does make your decisions feel different but ultimately superficial in retrospect. It's a tough design to implement properly for sure.
I can understand why designers avoid these mechanics as they're terrified of locking players out of content though personally I can admire them if they can pull it off (Dark Souls does this pretty well.) Thing is though, whenever do they give you a big choice it can be easily corrected down the road. Whether you kill Kaiden or Ashley in Mass Effect might as well be random choice as they both fill the same roles, granted they're both very different characters but one wished they provided vastly different content off the beaten path rather then have them fill the same gap in the overarching story. But hey, realities of game development and all that bollocks.
(On a side note, School Days has on official English version which might be worth looking into. Might give it a shot myself.)