The near certainty in the story that Vivi has died by the time of the end FMV sequence. I just don't know how I missed it. I've beaten the game at least twice, played it to some extent tons of times more than that, and it just never struck me. I mean, obviously the insinuation is there midway through the game when you first visit the Black Mage Village, but I always believed it to be ambiguous enough where I liked to imagine they found some way to keep him going. I never knew the end monologue was Vivi; I always assumed it was Garnet's monologue while still believing Zidane died, instead of the whole other context of it being the farewell words of someone whom themself is dying. This of course without the knowledge that the original Japanese text made it much easier to decipher who was the speaker due to specific pronoun usage that pointed to him. I don't even really recall noting the fact that he is indeed the only main character absent from the ending, rather its just little Black Mages, his "sons". But man, realizing it last night hit me hard! I've loved this little guy for so long, one of my favorite characters in all of games in what I consider not only probably the most underrated FF of all time, but one of the most underrated games period. But its just so weird being in the dark about something for so long.
In any case, a toast! To the best damn black mage in all of gamedom. I'm going to get back to playing now, because goddamn I still love this game. Its characters, its story, its themes. And if you happened to have wandered in here despite the spoiler warning: play this game. You won't regret it.