That is a common concept in nearly all existing videogames: you either say yes to accept a new quest or no to not take it. Players get used to this pattern by encountering it over and over, and finally simply start to assume beforehand that this pattern is also true for your game.
A good example of handling this problem is Deus Ex: Human Revolution. In the beginning of the game, the player is told to not waste time exploring and rush in for the quest, or else “people will die”. Many players simply assume that comment is simply an “in-game immersion” statement which wouldn’t affect the gameplay at any rate. Consequently, not two minutes after they are told that hostages were killed and they are too late, thus breaking the pattern players were used to very early in the game while still allowing them to rollback the two minutes they already spent exploring and instead prioritize the quest.
That could be a solution in your case. If many players think your game follows already established patterns, show them that it does not! Give them a small quest (or better yet, a few of them) that would require players to reason and use their judgement to make a choice, so that they get used to the new concept. You could also display a “help window” during the first time they get a quest that “not all of the quests should be taken” or “player shouldn’t agree to everything they’re told“. Once they are familiar with the concept, throw in your important quests, which they will immediately recognize as one of the problems they’d have to think about.
Another thing you might want to consider: if there is an important decision for players to make, give them as much information as possible and give them the time to think. That is, instead of having an NPC make a simple statement that looks like a quest offer (“Let’s try this totally silly thing!”), elaborate on what they’re offering and allow players to inquire for details and possible drawbacks. Make it feel like an important decision to be made, and your players will treat is as such.
Change the options to Left-Right rather than Yes-No.
A Yes-No choice is an option. Add this extra bit in or ignore it. A Left-Right choice is a choice. You can have this or that, but not both.
So instead of having a single character offer an option, have two characters offer conflicting paths. Make it clear that either way the play will miss out on some content.
I think this is likely to be treated as the classic good vs evil play style choice that many games offer. ie, players will assume that the story will remain essentially the same but with a different ending/character dialogue and put the choice down as a ‘no right answer’ dilemma.
So you may need to either tweak your ‘bad’ choice so it is not completely negative, or show players early on that there are game ending mistakes and they are expected to play it in a rogue-like way.
Also maybe you are just making a bad game. If you get to the very end after hours of game play and find that I can’t enter the evil lair because I did/didn’t do something seemingly innocuous hours ago. Is that fun?
Sure it might be realistic and challenging, but a lot of people will stop playing and write you a bad review at that point.
You would really have to make it clear that your game is more of a puzzle and you expect them to have to do multiple play throughs to solve it.
A way to show which answer is the “right one” without taking away the choice, would be to weight the options through meta-information.
Instead of just showing one “yes” option and one “no” option you can provide a list of options for the side you prefer.
- No. You’re going to get yourself killed.
- No. We don’t have time for that.
- No. That would put all of us in danger.
- Yes. I don’t care if you’re going to get yourself killed.
In addition to providing a hint, which option is considered the better one, it also gives you a chance to restate the consequences of the decision.
The above answer also takes advantage of a second learned convention from modern gaming: “Don’t judge logically, judge empathically”.
The “right” choice, more often than not, is the one that is empathic towards another characters plight. The phrasing of your answer should be done in a way, that makes it clear that this is the better choice for the character you’re talking to, not just yourself.