As you can see, there's lots of foreshadowing with respect of the plot of Ghost Trick, so... you can see the amounts of foreshadowing right here.
There is lots of this regarding Sissel's past.
The very fact that the dead can talk to each other, regardless of species.
Sissel can't read or recall what objects do or what certain terms mean while dead, yet every other dead character can. He figures his memory is fuzzy due to dying. This is not the case: he really can't read and honestly doesn't know what certain objects do, nor what certain terms/concepts mean, because like Missile, he is not human.
When you first meet Lynne, she messes up and mistakes herself to look like Inspector Cabanela. Later, it turns out that this is what happened to Sissel, who assumed that the spiky-haired blond man nearby was him.
After Lynne hides in the small elevator, she says she likes to crawl in small and dark places. Sissel remembers liking to do that too.
Cabanela mentions at one point that his coat is white, to show that there are no stains on it. Sissel quips that a black coat would be more practical. At the end, Sissel does have a black coat.
Inside one apartment Sissel can let a rodent be spotted before it lands next to the dictionary, and he notes that the boisterous writer treats it as something to be hunted instead of feared. Sissel says he can relate.
Very subtly, in the same location: when trying to get the phone over to Amelie, Sissel winds up inflicting all kinds of horrible injury on a rat without killing it. Almost like he's toying with it.
Another subtle example. During the prison blackout, one of the guards states that he wishes he could see in the dark, like a cat. Sissel quickly points out the similarity between night-vision and one of his ghost powers, which is of course awfully fitting...
When rescuing Jowd from the prison, who painted a portrait of Sissel, Jowd doesn't recognise the name when Sissel says he somehow knows him. That's because the blond-haired man in red that he painted was named Yomiel.
Sissel notes a couple times that he's developing a compulsion to knock down anything he can, which he attributes to his ghost powers becoming addictive. Actually, that's some more cat-like behavior.
At one point, to mean "out of danger", Sissel says "out of the water". A strange turn of phrase; shouldn't it be more like "out of the fire"? Not if you hate getting wet.
In the Special Prison, one of the prisoners is rocking out on his guitar, making a terrible noise. Sissel has absolutely no idea what he's doing, and guesses that he's making noise to get attention because he's hungry. Now, what kind of creature assumes making noise = being fed?
The titles given to the people in the records are never replaced with their real names. It's strange at first, but makes sense, given that a lot of animal narrators in fiction refer to humans as "that short one", "the chicken-eater", etc. instead of their real names. Not to mention sometimes the descriptions seem to imply that Sissel thinks that their job titles are part of their names. (E.g., "His name is "Detective Jowd.")
On a more general note, Sissel's personality is, once you know the twist, similar to the typical cat in fiction: aloof and unconcerned, but affectionate and friendly once a bond is made. Likewise, it's the reason Sissel considers Missile a little off due to the stereotypical dogs-versus-cats trope.
In Chapter 14, Missile's choice of words at one point is apt.
Missile: I can reach out my paw a little farther than you can, Sissel!
In Chapter 16, we have this talk:
Sissel: What do you suppose that shock was a minute ago?
Missile: I have no idea, of course. I'm just a little sheltered apartment dog!
Sissel: What with my loss of memory, I can't say I'm much better...)
Later on in the same chapter, when the submarine suddenly tips to one side just before Lynne can get to the exit hatch, Sissel's choice of metaphor is very telling:
Lynne: What happened now?!
Sissel: It looks like the submarine decided to rear up on its hind legs.
In some of the optional dialogue in Chapter 5, Sissel gives us this line:
Sissel: That cop looks miserable. He looks just like a drenched and dejected kitten in the rain.
There is an extremely subtle one regarding Sissel - Sissel saves nine people, just like a cat has nine lives. It's so subtle because you only have a couple of seconds between saving the ninth person and finding out Sissel's species.
If you return to the outdoor prison phone area with the moon in the sky above (where Jowd was arrested by Cabanela), Sissel remarks that there's no point in going there unless he wants to look at the moon again. As revealed later, Sissel has traveled and seen that moon before as a cat.
The security footage of Lynne shooting Yomiel has Yomiel leaning against a pole. After shooting him and being confronted by an assassin, Lynne backs up into the same pole, but moves away from it because it had barbed wire wrapped around it. And given what we later know about Yomiel's body....
Early on, while trying to get Kamila under the couch, Sissel said that it would be easier if he could possess her, but he can't do that. So Yomiel wasn't alone in wishing he had other powers.
Whenever you run into Beauty, she uses a strangely familiar way of addressing you. In retrospect, it becomes apparent that she thinks that it's Yomiel who keeps trying to spy on her.
Throughout most of the game, Sissel can visit the junkyard and have a short conversation with Ray to update him on the situation. Ray goes oddly silent and weak halfway through the game and soon stops moving altogether, which the player will most likely chalk up to the whole "dead tomorrow" thing. On the other hand, it seems Ray starts fading away around the time that Missile is run over in the park...
Speaking of conversations with Ray, if you go back to the junkyard and talk to him immediately after seeing the security footage of Yomiel manipulating Lynne into shooting him, Ray will tell you that "The truth is sometimes hidden in the shadow of what's being looked at."
After Lynne dies for the first time, Sissel will notice that her corpse is not giving off the strange waves his own corpse is. Sissel assumes this is because he has the powers of the dead; Ray does not confirm why this is.
When the flashback of Missile dying is shown, his body does not give off the same waves that Yomiel's body does. Instead, the Temsik rock gives off the waves. Yomiel's body gives off the same waves for a reason.
The medical examiner comments on overhearing the two detectives at the same time as Sissel, establishing the minor Running Gag of Sissel and someone alive echoing each other. of course, he's not your average bystander.
Also, when examining Lynne after she's shot, his 'examining' animation puts his stethoscope in places it has no business being. This isn't an accident. Cabanela later comments the examiner's incompetence outs him as a fraud.
In the very beginning of the game when you possess a guitar instead of an out-of-reach wrecking ball, Ray expresses surprise. "I see... A guitar, then, is it? Ahem." It turns out Ray is actually Missile, whose ghost powers have a longer range than yours do.
Why do the prisoners get luxuries like music equipment, being able to paint, and a strange mind machine? Because it's suspected none of them are actually guilty of their crimes, and the police are trying to figure out what the true cause was.
Attentive players can figure out Lynne didn't intentionally kill Sissel (actually Yomiel, though she also didn't intentionally kill Sissel either) as soon as the video tape evidence is first shown, because the first shot misses due to Lynne clearly struggling with the weapon rather than shooting with the determination you'd expect from a real murder. Also, the entire time Yomiel is calmly leaning against a pole rather than fearing for his life, indicating he wanted to be "killed". Much later in the game, it's revealed that Yomiel's body was empty whilst he was possessing Lynne, meaning she was essentially just shooting a propped up "corpse" at that point.