It's worth thinking about. The real problem with a common story that incorporates both routes is not really that players might pick the wrong stuff and end up in wrong routes. That's easy to deal with. The biggest issue in any game that offers routes like (love vs corruption, good vs evil, male dom vs fem dom, NTR vs non-NTR) is maintaining the correct character progression, motivations, personality, and story progression. This is because there will obviously be common lines of dialogue or internal monologues that are independent of variables. In so many games, these common lines of text are leaning too much to one route or even inconsistent with possible events that happened on various routes. The MC might look bipolar and all over the place mentally. The girls might act in the wrong way.
There are a couple ways devs try to deal with such issues.
- Make the common route dialogues neutral so that it could fit both routes. That said, trying to do this in and of itself is a constraint on the set up and progression of both routes when it's diametrically opposed. That leads to the next method.
- Make a shitload of conditionals. Whenever you have a conversation, check for flags and variables to display the fitting dialogue. Check variables and conditionals to change the events that trigger. Make conditional internal monologues.
That #2 method is essentially similar to route locking in effect (if a player picks consistent choices for a route). It does let you be more fluid in going in and out of routes and things like that, but it's a huge amount of work. If you were doing a dom route, but throw the run and slip into NTR later on, can the game keep track of this turn of events and react accordingly? We can also look at the possibility you laid out. If you dominate the wife but the daughters are NTRed, that would be a HUGE shift in the relationship dynamics of these characters. You need to essentially create a unique route for that possibility and every other combination, OR you need to keep all those characters compartmentalized and unable to interact too much with each other. So we end up with the dilemma of making concessions in storytelling or adding a truckload of work in coding and writing the variations (Check out Our Red Strings for an example of massive conditional variations).
I think a single story with variations can work for personality types like good vs evil. It's obviously used in the vast majority of choice based VNs to various degrees. NTR is a special case though because it requires so much set up and dedicated progression in the story. Plus, NTR is diametrically opposed to a Dominant MC route. I can kinda see NTR vs loving husband/father work out in a single plot. A loving husband is generally an easy target for NTR, so it shouldn't feel that out of place if you slip into NTR later on after building up a loving relationship. I personally don't like asshole/dominant MC getting NTRed in general, so maybe take this next point with a grain of salt. I think it would be harder to make a consistent story that mixes this type of MC with a possible NTR route.
Basically, route locking is a shortcut for the dev. You can make a very different set of events and story progression on those routes without too much worry (although that leads to more writing as well). It's less elegant, but probably MUCH easier to manage for a first time dev.
Sorry for the long ass posts. It's just my personal opinion. There is no right answer. Anything is possible, but some plans require more work for potentially greater payoffs.
