I've only skimmed since I don't want spoilers, but the heart of the issue seems to be the question of certainty with relationships. Do I want all of the NPCs to be interested in the protagonist, regardless of gender?
I think it would be best to look at Fallout: New Vegas. They handled all sorts of sexual orientations and situations. You couldn't romance anyone, but I think that did it a service. You had straight companions, gay companions. I spent fourteen hours of real life game time with Arcade Gannon before I realized he was a homosexual. I spent ten minutes barking up the wrong tree with Veronica before I had to give up.
Certainly a novel approach on the matter. This has the added bonus of surprise and gives a stronger feeling of character depth, with the drawback of requiring multiple playthroughs to see each possible outcome.
Many games have been designed lately to require multiple playthroughs. Good endings, bad endings, and so on. In my opinion, the best have good ways for you to see every ending with only one playthrough, if the game is mostly linear up to the end. The Deus Ex games have this, and the latest DX has the ending autosave at just before the big decision, so you can continue to use your latest save to watch every ending.
Now, I personally have little objection to being protagonist-sexual. The entire point of a video game, just like in well-run RPGs, is that you're the star (or a group of stars, in RPGs), and the world revolves around you. Most novels either do this directly, or they have a character like Dr. Watson who follows around the real star, Sherlock Holmes.
However, I can understand how it might strain incredulity to have characters suddenly shift during a series. If it might help, you can imagine that perhaps the NPC in question was always hiding a secret crush, wanting to say something but never able to find the words, until either summoning the courage or being approached by the protagonist.
For example, in Dragon Age 2 (to once again bludgeon that example of all that is wrong with bioware post-2010), It is only if you're playing a male character that the characters of similar gender mention that, at points in their past, they've had relations with other members of that gender. (Eg. Only if you're playing Male Hawke would anders assert that the mage Karl was the one who took Anders' virginity, and Fenris would claim [with some pride, no less] that his duties while a Tevinter slave included bending over for his master and his master's male friends.) If you play as a Female character, it is considered, by the game, as if any homosexual relations mentioned by that pair were completely and utterly untrue.
I consider this to be not so much a fault of adding homosexuality to the games as that, because there are so many choices inherent in the Bioware games, everyone really does get a very different experience. Bioware goes above and beyond in individualizing your game experience, which allows you a very personalized game, but also can rob you of the feeling of camaraderie with friends, where a movie is experienced exactly the same by everyone, and linear games follow a similar suit.
This has been discussed by system gamers playing through modules. If everyone has played through the Dank Dungeon of Evernight, even if it was run by different GMs, you can talk about how tough the Creeper was or how nasty the traps were. With movies, you can share the experience of how the vampire ashed himself in the sun just so that she wouldn't get turned on the third night after the biting.
In some ways, this can make the replay value better, but I can certainly see how flexible it would make the fourth wall if you can't help but notice all the inconsistencies. Fallout New Vegas' method would be much better for multiple replay value, with Bioware's games adding more possibilities for a single runthrough where you don't care if you see everything.
I can definitely see an irony, there, since you'd think more flexibility would allow for more playtime.
I'm therefore going to make this recommendation: some games have language blockers, where you're asked at the very beginning of the game if you want there to be naughty words. It should be very simple to have the choice between protagosexual NPCs and pre-selected sexualities. Mr. Cuddles is gay up until someone selects female and selects protagosexual, and everyone is happy. The "hardcore" gamer fan base will likely stick with pre-selected. It shouldn't be much harder than just adding in an If-Then tag on each NPC's sexuality subroutines.