I don't know. I think I understand what you're trying to say, but I also think there are some assumptions here that aren't necessarily true.
A big one is that the villain is plotting anywhere near as well as they think they are. They're usually not. It sucks to play a character like the ones you're talking about here and have to ignore a plot with a very obvious killer or kidnapper because the player doesn't want any consequences and keeps insisting that their suspicious character is ~enigmatic~... but forgot to make sure that means, motive, and opportunity can't be tracked back to them.
Sometimes they are genuinely enigmatic and the plot covers all the bases, but that doesn't seem to be as common as many villain players would like it to be. It's hard to plot something like this out successfully without something being forced. It may work better in a larger game than a smaller one, because it's easier for a bad guy to get lost in a crowd, but when the time comes for shit to go down, a bigger game means more variables to think about.
Another assumption is that the characters you're talking about are static and not capable of learning through observation, but most of them should be fast learners. Someone mentioned Holmes not knowing that teleportation could be an explanation for something, but unless your villain is the only character in the setting who has powers, Holmes is going to know not long after his intro that other characters in the setting do. If walking through walls is the only good explanation for a situation, and he knows that other characters can fly, burn holes in things with their eyes, and read people's thoughts, he's going to have to play with the idea that someone might have either teleported or phased through matter. That's not enough to prove anything on its own, and it's not something he should automatically jump to, but it's an idea he should entertain eventually if it fits. Then he still has to figure out who can teleport or phase. That could be the subject for an extended plot.
A third assumption is that the villain didn't have to go through the same learning process and is leaps and bounds ahead of everyone else. That may be true, but it may depend on which character has been around longer. Holmes who just did his intro last week doesn't have a leg to stand on. Holmes who has been in the game for a year against a villain who has been there for three months might. Then again, the villain who's been there for three months and hasn't showed his ass might still be enigmatic.
A fourth assumption is that the villain is going to be "just as effective as they are in canon." The truth is, they have the same disadvantages that you've listed for Holmes and Batman. This may not be a handicap if they just want to drag random people down dark alleys and kill them, but a lot of supervillains rely as much on money and influence as Bruce Wayne does.
A lot of this can't be generalized and depends on the details of the plot, the game, and the characters involved in it.
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A big one is that the villain is plotting anywhere near as well as they think they are. They're usually not. It sucks to play a character like the ones you're talking about here and have to ignore a plot with a very obvious killer or kidnapper because the player doesn't want any consequences and keeps insisting that their suspicious character is ~enigmatic~... but forgot to make sure that means, motive, and opportunity can't be tracked back to them.
Sometimes they are genuinely enigmatic and the plot covers all the bases, but that doesn't seem to be as common as many villain players would like it to be. It's hard to plot something like this out successfully without something being forced. It may work better in a larger game than a smaller one, because it's easier for a bad guy to get lost in a crowd, but when the time comes for shit to go down, a bigger game means more variables to think about.
Another assumption is that the characters you're talking about are static and not capable of learning through observation, but most of them should be fast learners. Someone mentioned Holmes not knowing that teleportation could be an explanation for something, but unless your villain is the only character in the setting who has powers, Holmes is going to know not long after his intro that other characters in the setting do. If walking through walls is the only good explanation for a situation, and he knows that other characters can fly, burn holes in things with their eyes, and read people's thoughts, he's going to have to play with the idea that someone might have either teleported or phased through matter. That's not enough to prove anything on its own, and it's not something he should automatically jump to, but it's an idea he should entertain eventually if it fits. Then he still has to figure out who can teleport or phase. That could be the subject for an extended plot.
A third assumption is that the villain didn't have to go through the same learning process and is leaps and bounds ahead of everyone else. That may be true, but it may depend on which character has been around longer. Holmes who just did his intro last week doesn't have a leg to stand on. Holmes who has been in the game for a year against a villain who has been there for three months might. Then again, the villain who's been there for three months and hasn't showed his ass might still be enigmatic.
A fourth assumption is that the villain is going to be "just as effective as they are in canon." The truth is, they have the same disadvantages that you've listed for Holmes and Batman. This may not be a handicap if they just want to drag random people down dark alleys and kill them, but a lot of supervillains rely as much on money and influence as Bruce Wayne does.
A lot of this can't be generalized and depends on the details of the plot, the game, and the characters involved in it.