But I'm not a big fan of a danger sense point system similar to luck, serendipity, and all of the other metagamey stuff you can by to help plot protect your characters.
No, I think you need to think more intuitively.
As in, Intuition.
Intuition allows a player to make an educated guess/hunch on a topic that doesn't build off of existing knowledge. The GM makes a secret IQ roll with a modifier equal to the number of "good" choices minus the number of "bad" choices. For example, if the PC is wondering which car in a parking lot full of seven cars is the one stashed with drugs, it would be a -6 to the check (1 right car, 6 wrong choices, 7 total).
Danger Sense can be much the same, where players have to actively decide to use the ability. Sure, this weakens the ability to an extent as a means of protecting a character played by a players who might not be very cautious, but Danger Sense also doesn't inherit penalties to perception rolls like Intuition does with IQ rolls. A character with high perception will reliably be able to tell that something is just... off. Any other character wouldn't even have the option of trying such a thing without having a relevant skill, much like characters can't attempt intuition without the advantage itself.
Now, for limiting Danger Sense, I have two main suggestions:
- Only allow one Danger Sense roll per situation/scene. An entire combat is likely a scene, sweeping a warehouse is likely a scene, a meeting is probably all a single scene. Now if a gunship helicopter suddenly arrives during any of those scenarios, that might warrant being able to check again to see if the character gets a sense that maybe they should get the hell out of dodge.
- Limit perception for use with Danger Sense to ~14. Characters can have higher perception, but for Danger Sense checks, anything 15 and above fails. (Although I'd be tempted to limit to 12, which is a 74.1% chance of success, where 14 is a 90.7% chance of success.) Alternatively, you could assess penalties and bonuses on situation, but that's probably up to personal preference.