Looking around the forums i realized that few people know much about Shiki. I'm an avid fan of Type-Moon and here I'll tell you guys all about Shiki and why he is so imba.
Background: Shiki was the son of Nanaya Kiri, the last head of the Nanaya clan. The Nanaya clan fell to the Tohno clan and the Kishima clan (sub group of Tohno). Tohno Makahisa adopted Shiki just because he had a son named Shiki also. (Original Shiki = SHIKI, Nanaya Shiki = Shiki).
After about 8 years, Shiki, SHIKI and Tohno Akiha were playing in the yard when SHIKI's inversion impulse hit him. An inversion impulse is when the demonic blood of the Tohno clan gets awakened after a period of time. Protecting Akiha, Shiki died in her place. Makihisa arrived and beat down SHIKI and healed Shiki, after which he sent Shiki to a foster home (Arimas). When Shiki wakes up at the hospital before going to the Arimas, he sees lots of lines over the walls, bed, doctor, everything. After running away from the hospital, Shiki met Aozaki Aoko, who stole a pair of enchanted glasses from her sister. Aoko is one of the four "sorcerors" in the world. (Sorcerors are not magicians! They are not bound by the rules of the world, unlike magicians.) With her powers, she made the glasses have no "fate of eventual death".
8 MORE years after that, Shiki returns to the household with no memories beyond 8 years ago. Some stuff happens; (vampires, church exorcist and two maids, read Tsukihime for full story), and Shiki thinks that he's quite insane. In reality, it's the Nanaya blood in him continually telling him to kill his half-demon sister, Akiha.
Now, onto his eyes and such, and why it SHOULD be Nanaya Shiki.
His eyes are normal eyes, embedded with a magic circuit, that allows him to see the "fate of eventual death" on all existing things. This power allows him to "kill" anything, not just living things. He can "kill" a wall, and the wall will break/crumble. He can "kill" nature, because it has an "existence", and a "concept", so he can see its eventual fate of death. This "fate of death" is sometime between now and the end of the world, where the world dies.
The "fate of eventual death" manifests itself in his vision as line and dots, lines being "the place where things can be broken", and dots being "the total of this being's existence". When a line is cut, physical damage occurs; arms fall off, walls are sliced and so on. The dots, however, are different. When they are pierced, the totality of the "object/being"'s existence is destroyed. this translates that the entire thing would just crumble to dust as though it had never existed.
Dots being pierced are absolute, and cannot be recovered. This works on magic, reincarnation, immortality, and so on, because it destroys the "Existence" or the object and not the "life".
Now, onto Nanaya/Tohno Shiki.
There are 3 different sources that need to be taken into account because they are all canon.
Tsukihime's Tohno/Nanaya Shiki:
In Tsukihime, Tohno Shiki does not know the existence of Nanaya. He thinks himself to be Tohno Shiki, and Nanaya Shiki never appears in person in Tsukihime. It is a fact that when Tohno is in life threatening situations, his "Nanaya" personality will appear, and he'll feel an urge to kill, maim, and slice things. Also, it increases his reaction time and agility by more than tenfold, to place him on par with the vampires and such that he fights.
"Nanaya Shiki" only once truly manifests in Tsukihime, when Tohno Shiki fights Akiha in Kohaku's arc. Tohno himself can feel a different personality inside of him, and it's close to schizophrenia, as his two "personalities" grapple with each other in their mind to gain control of "Tohno Shiki"'s body and kill/not kill Akiha.
It is stated in Tsukihime that "Nanaya Shiki" does not truly exist, and is a "possibility" for Tohno Shiki to have become Nanaya Shiki, and it was if the Tohnos did not attack the Nanaya clan, and if Shiki had not met Aoko. Shiki would then have become "Nanaya Shiki".
Kagetsu Tohya's Tohno/Nanaya Shiki:
Kagetsu Tohya is a semi-sequel to Tsukihime. Shiki finds himself in a dream created by someone unimportant to this discussion. Several times throughout the game, he meets "Nanaya Shiki" as a physical being. This is explained by the fact that Nanaya Shiki was a subconscious "nightmare" of Tohno Shiki's, and when he entered the dream world, his "nightmares" and "Dreams" followed him in. Even so, Nanaya Shiki is treated as a real person in Kagetsu Tohya. This version of Nanaya CANNOT SEE LINES/DOTS OF DEATH, AND DOES NOT POSSESS Shiki's MYSTIC EYES OF DEATH PERCEPTION.
Melty Blood's Tohno/Nanaya Shiki:
Melty Blood is a partial spin-off 2D Arcade fighting game, and contains most of Tsukihime's and Kagetsu Tohya's important characters. The Nanaya Shiki in this version is even more physical, as he exists and can fight any of the characters in any location. This version of Nanaya Shiki CAN SEE LINES OF DEATH, AND POSSESSES Shiki's EYES OF DEATH PERCEPTION. However, he chooses not to use it as his own abilities already allow him to be on par with most of the other characters, going so far as to even remove it from his most powerful attack.
Now, onto why it should be Nanaya Shiki instead of Tohno Shiki.
Firstly, look at his attacks. One of them has him saying something close to "Choubi Hassen, mujou ni fukusu", which is Nanaya Shiki's second most powerful move in Melty Blood. The sound effect/voice is taken directly from the game. Next, we have Nanaya's ulti. It's "Kyokshi, Nanaya", which means "Extreme death, Nanaya". It is his most powerful attack from Melty Blood and it is supposedly instant kill. (Not in Melty Blood, in Tsukihime/Kagetsu Tohya)
Secondly, look at his skill icons. The icons for the skill have a picture of what seems to be Tohno Shiki, until you compare it to Nanaya Shiki's portrait. It is obvious that it is in fact Nanaya Shiki as his eyes are narrowed into slits instead of Tohno's rounder eyes.
One more not so obvious point is that FoC's Shiki's movement animation is a direct copy of Nanaya's Melty Blood animation, complete with sliding forward when stopping.
Therefore, the above evidence shows that it is indeed Nanaya Shiki instead of Tohno Shiki, and Tohno/Nanaya Shiki are two distinct and different persons.