The big thing is how a game structures its facts when you want to have clue scenes.
The GM decides what happened beforehand, and now the point is to have all clues and witnesses eventually point towards that fact. This is the most common way games handle things, but there is rarely good advice towards doing it well.
Start with Free Clues
Be sure to give players several free clues or facts in any scene they arrive in. These should require no skill or training whatsoever. You may choose to give more to characters who are trained in certain skills. Free clues require no roll, do not require players to say specific actions ("Oh, you didn't SAY you were looking under the carpet..."), but assume the character is competent and comes across these things. The free clues should not be false; they should be accurate, if incomplete.
Additional clues are given for appropriate searching, questions, and skill rolls as appropriate.
Witnesses are Forthcoming
Witnesses generally WANT the PCs to know something. They may tell everything they saw, but what they saw was incomplete. They may tell background information (i.e. "Those two were always arguing." "I think they had money problems."). They may tell part of the truth to advance their side of an issue or to hide some wrongdoing or shameful fact on their own part.
If a witness is lying or hiding something, you are best off telling the players, "It seems as though you're not getting the whole truth here. You're pretty sure this is generally accurate...but something is off." The players can later figure out how they're going to pressure the witness or verify facts on their own outside of this.
This is not because the PCs are mind-readers, but more importantly because the players are not mind-readers. The players should trust you, as a GM or narrator is giving them generally accurate information. This ALSO helps point the players in the right directions at where to look for clues or how solid to take anything they get. (Dogs in the Vineyard is the game that suggested this, and I recommend it everywhere now.)
Assume Competent Characters and Insider Information
If a character has a criminal background? Start giving them ideas based on their experience and the way they'd look at the situation. The character with a really high driving skill probably knows a lot about cars in general. The noble blooded investigator can identify specially crafted luxury items, etc.
Tailor the description to the characters. The information is not just about objects and history, but also about social scenes around these things as well.
"The scratches in the wall are weird, jagged. You look at the floor around it and find a bent nail, caked with a bit of plaster... and blood. Someone used a spiked bat, a cheap improvised weapon, definitely someone planning to hurt someone. This was a messy job, not a professional for sure. You can rule out the Espinozas - they wouldn't have been this stupid."
Motivations are Key
Figure out the motivations for the people involved. That's the best selling point. Most mysteries are built on greed, fear, jealousy, animosity and resentment. Notice how different this is than the usual rpg trope of "They were secretly trying to do something to do something with magic." When you do this, and put the motivations at the center of things, it becomes an exploration of who the NPCs are, rather than just "event X happened at Y location by Z person".
Dogs in the Vineyard lays out its "Towns" this way - you figure out that someone was a) breaking the traditions, and b) someone was being mistreated (sometimes it's the same person, sometimes not)...and just as often c) there was a reaction that may have been violent, extreme, or dysfunctional.
Sorcerer (in the Sorcerer & Soul supplement) uses specifically built relationship maps - tying together anyone who is related by blood, anyone who is romantically involved, then looks at the emotional ties/motivations above and beyond that. Who is doing something wrong, or hurting another, and what comes out of it, based on the tropes of detective noir mysteries. Often the criminal act ends up being very secondary to the real dirt going on between the people.
The Pre-planned Scenes Pitfall
Although you can have pre-planned events that the players are investigating, pre-planned scenes don't work as well. Many games attempt to create a linear or branching set of scenes the clues are supposed to point players towards, but this falls apart for several reasons:
1) Players may get on the wrong idea, and you end up having to railroad them into a correct path of investigation to get to another scene.
2) Players may use abilities or simply correct deduction and leapfrog several clue scenes, in which case, you have to railroad them into not solving things ahead of the planned scene build.
3) "Clue to clue to clue" is not actually a great narrative device. It shows up in action and pulp stories, mostly because the point of those stories isn't a good mystery or investigation, but simply excuses to show off a lot of locations and action. It really feels pointless, like getting strung along bad side-quests in a video game.
Games that allow you to improvise scenes work better. Players can come up with all kinds of methods of investigation: flipping a witness or accessory to a crime to helping them, finding unconventional ways to access information or follow clues, and of course, ways to solve a problem as well. And you're not stuck trying to find reasons that these don't work or waste time trying to push players back onto track.
There's several games which allow players to narrate facts on the fly, or allow the GM to simply create facts in the moment instead of pre-establishing them. Often these games tie the fact making into the mechanics, which makes the pacing and presentation a non-issue, and mostly the difficulty at that point becomes making sure the group ties together a coherent set of clues and doesn't splinter into people pushing the facts into different directions that makes a mess.
In these games, the GM's role is changed; you're following the outcomes the players are giving you instead of trying to find ways to throw clues at them. Since everyone is creating and improvising the facts together, no one knows the real outcome or answer to the mystery until it is solved which makes it pretty exciting for everyone involved.
Inspectres is a game that builds it's investigation completely on this and might be worth checking out as an example.