There were a few perks in Fallout and Fallout NV that seemed a little off to me... some of them seemed like things that you should be able to do off the bat, or as quest rewards.
These were things like the Cyborg Perk in fallout 3, the cannibal perk, and the GXR Implant. I think if they were ether rewards, or even had some background to them, it would be not only awesome, but also show some exposition to who the Sole survivor is.
If you were to keep it a level up perk, For instance, when the Cyborg perk is ticked, after the level up screen and all is over and done, and if you're under the condition of being safe/out of combat you witness an animation where the PCs skin in an elbow break and comes off, and it exposes a mechanical terminator set up of metal in cased in meat, your PC looks at it and they have a flash back, a prerendered movie that takes a few seconds to play back, maybe to you're prewar days with some kind accident that results in seeing you're character getting a limb seethed off, getting carted off to help, and some kind of invasive surgery taking place.
or maybe there could be a first person animation on the hud where you suddenly get a boot up screen telling you that your Cyborg implants from a time you seem to have forgotten about have just activated, your PC may have forgot about them due to Cryo, or the Trauma of the operation.
Also I did like The way Cannibalism was handled in skyrim, and I do hope it makes its bloody return - something satisfying eating all the raiders in the world. I was thinking though rather than some one "tricking you" into thinking about a time you ate human flesh, you could witness a similar preenderd imagining where in prewar days something happens to the player and they happen to eat human meat, maybe advertised to them at some dodgy food place as long pork, or a swapable clip where if you encounter human Hunter, and they offer some of at "meat that's sweeter than most" you just witness them offering you some meat and eating it.
just some 2 cents...