In Japan, around 2005, Metal Gear Solid 3 received a tie-in DVD box set (I'm not exactly sure what it contained, so I won't speculate) which contained a book: "SHEDDING". It wasn't translated until 2022, last summer (credit to @NilsPommerenke).
I only just discovered "SHEDDING" today, although I'd inadvertently read excerpts from it before, contained in Bryan Hikari Hartzheim's biography of Kojima; they detailed his experiences with Ryohei Shogaki and Naoki Matsui. I remember reading that the three had a special brainstorming process ("jetstream attack"). "SHEDDING" clarifies that it's named after something from Mobile Suit Gundam. Too bad that didn't make it into the biography, it's cute!
Anyway, within this over 150-page document lies an interview with Akio Otsuka, Snake's Japanese voice actor. It's during this interview that Otsuka casually drops the origin of Snake's famous catchphrase: it's a reference to a colleague of his, Issei "Shark" Endo.
INTERVIEWER: Although readers cannot hear Otsuka-san's voice in person, I am sure that Snake's voice is echoing in their heads, "Kept you waiting huh?"
OTSUKA: Actually, the line, "Kept you waiting," is a rip-off (laughs). A friend named Issei "Shark" Endo, already in his 50's, narrated the first commercial for JR Tokai's "Cinderella Express" and is now a master of commercial voice acting as well as a musician. When invited on stage at someone else's concert, he would show up in the middle and say, "Kept you waiting, huh?" (laughs). It had quite an impact on me, so I asked him if I could take and use it. Director Kojima was very pleased.
A few quick web searches (including a 2020 podcast episode with Otsuka) reaffirm that Shark's catchphrase, "待たせたな" (matasetana), is undeniably the same phrase spoken by Snake during the first codec call of MGS2. It's so interesting that such an obscure reference (even in Japan) was able to become so legendary amongst gamers, almost certainly outsizing Shark's fame, despite being completely lost in translation. Even Japanese netizens have barely heard of this.
Speaking of being lost in translation... Snake actually says his catchphrase twice in MGS2, but the second appearance was, of course, precisely the victim of that (credit to @Arc_Hound). Instances like this make me realize the near-futility of trying to enjoy not just translated works, but aging ones at that, especially those from Kojima. His games, built on decades-old pop culture and self-references, cannot be fully enjoyed in anything but their native Japanese. For example, during the climax of the Tanker Incident, Ocelot directly quotes Liquid; a few scenes later, Liquid directly quotes Fox (credit to @jankahl). In English, these lines are totally different between MGS1 and MGS2, and while they have similar meanings, the direct reference is lost, to the detriment of the player.
Anyway, that was cool as fuck!? Now I and the rest of us Anglos finally know what the origin of Snake's famous catchphrase is, and can even hear the "original guy" say it his way!