Maison Ikkoku/WMG

Yotsuya is Golgo 13
Think about it: He has a job that requires him to work odd hours and which he can not reveal anything about. He demonstrates remarkable stealth when he wants to, and is never at a loss for words.

And look at those eyebrows! It's staring you right in the face!

Yotsuya is a Time Lord.
IT EXPLAINS EVERYTHING!
 * How does Yotsuya manage to live (and, presumably, pay the rent) without any signs of steady employment, or even a normal daily routine? Obviously, he completes his business by using his Time Lord powers, leaving the other residents of Maison Ikkoku none the wiser.
 * Room #4 is his TARDIS. This is why, on the rare occasions the inside of his room is seen (such as the egg episode and the Yagami tutoring episode), it looks completely different...they were just two parts of the larger complex.
 * Time Lords have a longer than average lifespan. This explains how, when Kentaro found the photograph album, there were pictures of Yotsuya going back to the 19th century, yet looking completely the same. (What, you actually believed the explanation that it was his family members? No two people, however related, resemble each other quite that much.)
 * Telepathy is another power of Time Lords. How else could Yotsuya know the exact moments to do a Stealth Hi Bye and catch Godai in a blackmailable state, often in the middle of the night or in completely unrelated parts of town? This happens way too often to be coincidence.
 * Like the Doctor, Yotsuya's true name is too bizarre or unpronouncable for daily life. Hence his use of a simple pseudonym, and his lack of interest in giving out a first name. (Alternately, Yotsuya's statements that his first name "is spelt like X and pronounced like Y" are actually true, and it's just that humans haven't figured out the complexities of the Gallifreyan language that would make this intelligible.)
 * From The Other Wiki: "Time Lords are an aloof people, with a society full of pomp and ceremony." Sound like any traditional clothes-wearing, formally-speaking, haiku-quoting person we know?
 * Finally, a travelling Time Lord needs a pretty Companion...Yotsuya has Akemi. Or at least, he thinks he does. Unfortunately for him, she's also working for the Master...