Writing in RPGs can be tricky. Jokes don't always age well, and a joke character can very easily tread into stale. In Final Fantasy VI, I believe that Ultros comfortably falls into the former and not the latter.
Truly an anomaly, Ultros has no reason for doing what he's doing other than to just mess with the party, and it just never gets old. I have no idea why "big purple octopus who keeps threatening to eat the player" works as well as it does, but it does. It sticks, and they play it just long enough. The sixth entry in the Final Fantasy series is one of the heavier ones in terms of story, so Ultros' comic relief role always comes off as more entertaining than annoying.
That being said, he's no Negative Man, but who is?