Missing the Clue
The Esoterrorists's mechanics are largely based around a single idea--it's hard to run mystery plots in typical RPG games. Typically, the characters must make rolls to discover clues. If they fail their rolls, then they don't uncover the clue, and the plot grinds to a halt.
The Esoterrorists (and other games using the Gumshoe system) solve this problem by guaranteeing that characters can find important clues. Your investigative skills give you a pool of points. You can spend these points to automatically discover clues (and sometimes additional details). This guarantees that the plot will continue to move forward.
Now, that's not a bad mechanic, as far as things go. It looks like a great way to run mystery games. But, I'm not sure I agree with Robin's analysis of mystery games.
True, mystery games are often incredibly frustrating. But, I don't think the dice are to blame.
Sure, it sucks when characters miss an important clue. And maybe it matters, if you're running a simple whodunnit. If the bad guy has already killed all the people he intends to kill, then one missed clue and he might get away. However, that's not the type of mystery I want to run. I prefer mysteries where the characters are peeling away layers of a larger conspiracy. Sure, they may not be able to solve a single murder--but, just wait. There will be more.
If the characters botch a single roll, don't sweat it. Just quickly move time forward to the next incident.
The bigger problem is pacing. The GM is the only one who knows the full story. Ideally, he should dribble out clues at just the right rate. They should come fast enough to keep the player's engaged in the story, without giving away the ending too early. This is incredibly hard to do. And I'm not sure The Esoterrorist's mechanics can really help here.
Here are some suggestions:
1) Give the characters clues that are hard to understand, but that open up possibilities for further research. The classic example would be some sort of occult mark on one of the victims (or bad guys). The characters have no idea what the mark means, no matter how good they roll (at best, it seems somehow familiar, but they can't put their finger on it). The clue remains unsolved, but opens up opportunities for future research or investigation.
The main goal here is to have the players proactively direct the investigation. This helps with pacing, since the players will pursue those things that most interest them. Proactive players help define how quickly the story unfolds. And, once players start acting proactively, they will usually find ways to ferret out all the clues they need.
So give them clues they can follow: A phone number ripped from a phone book, The picture of a famous celebrity, taken from a cell phone camera, An informant turning up dead. The opportunities are endless.
2) Reward the players for being proactive by providing them with additional clues. Always remember, ever scene should move the story forward. In the case of a mystery, each scene should provide one (or preferably more than one) paths that the characters can pursue further.
Also, you don't have to force the characters to roll for every clue. You can reveal clues as part of the description (or clues to clues). Let's say there's a few bloody fingerprints smeared on the window. You could mention that there is blood on the window when you describe the room. Or just mention the "dim light filtering through the smeared window", and wait for the characters to ask about it.
When someone actively investigates the window, you may or may not require a roll to identify the smears as blood (or to notice the fingerprints). Obviously (at least obviously to me) if someone asks, "are there fingerprints on the window?", just say "Yes" and move on.
Don't let yourself get bogged down by the rolls.
3) Be stingy with the clues. RPG players are typically very smart. Don't make it too easy on them. It's better to be too stingy than too generous, especially since you can always spice things up (see hint 4).
4) Don't let the plot slow down. If things start to drag, have something exciting happen. Maybe the conspiracy thinks the players are getting too close, and tries to off them. Maybe they take the next major step in their evil plan. It doesn't matter. Pick something that gets the blood pumping again and keep things moving.