Here's an option I thought up:
Stalker gets into a fight; if by the choices the player makes he wins, he continues on with existing quests; if he loses, he is thrown into a dungeon, made a slave, or whatever, and he needs to escape or be rescued (Shani?), which would be a new quest to be completed before Stalker could continue with other quests.
Since this is a sandbox game, not a strict VN, such a scenario would not be too difficult to implement. The catch would be in how much extra content would need to be added for the capture route, and if any of it's sexual in nature, people would complain about missing content by winning the fight. And if the developers compensated by making it so that Stalker had to miss some quests if captured, then the players would have to play two routes to see all content.
The moral of the story is that all options/choices may have unintended consequences for both the developers and the players.
Afterthought: I like my scenario so much that I'd like to see it implemented, but so that Stalker loses no matter what and has to be rescued by Shani. [I don't like to have to go through separate routes for important content (sex scenes
)]
At any rate, the developers will do what they will, and I'm sure I'll like it, whatever it is.