You bring up some interesting points. What I see as the issue is that either:
1. These are "bugs" in the form of missing connections / flags that can be added.
2. These haven't been planned for, and thus even if the connections were created, there wouldn't be any voice acting to go along with it.
Probably some combination, but more of the latter is much more work to turn around. It's very easy to see where the complexity of choice makes all possible player choices very difficult to cover.
Keep fighting your fight, hopefully we'll see these improve over the next year.
