While I'm posting this with 'Vampire the Masquerade' in mind, it applies to any rules system that uses vampire staking rules.
First of all, I want to clarify that I don't mean staking a vampire while he's sleeping or otherwise vulnerable.
No, I mean staking a vampire mid-fight, or when the vampire is otherwise ready for conflict.
To me, having rules that can stake and paralyze a vampire mid-fight is the same as having rules for, say, a headshot during a gunfight, or simply stabbing a normal dude in the heart with a knife. What I mean is that very often, games that include vampires will also include rules for staking them. Sometimes the rules require that the wound inflicted by the stake is the final wound required for the character to be defeated anyway, and it basically just means it has to be by stake specifically. Other times, like in V:tM, you can do it as a single attack, and if you succeed you won the fight. It's difficult in V:tM, I'm not saying the opposite. The attack has to be at a difficulty of 9 and you need to cause three health levels of damage for the vampire to be staked and paralyzed.
I think it's fine to have such rules. The problem is when all the other beings in the game, including plain humans, don't have to deal with the same rules. It actually makes the vampire characters more vulnerable in an odd way. You CAN skip the normal combat conditions and just stake a vampire through the heart, but you can't just shoot a normal guy in the head? Again, not really a flaw in the game, just a problem if the Storyteller/GM doesn't acknowledge this.
You want to knock a guy unconscious in one attack? Difficulty 9, three levels of health. You want to shoot him in the head? Same. Because at the end of the day, undead vampires shouldn't be the ONLY guys you can take out in one shot.