I think the point of this topic was the ending that occurs after [beating the final boss], not the process of doing so or even the final dungeon leading up to it. In the case of FF9, the ending was long and dynamic and certainly something different, regardless of whether gamers were confused by the sudden appearance of the last boss. A problem most large, longwinded RPGs must confront is having to tie up all the loose ends in several minutes of footage. Final Fantasy has learned how to handle this by throwing in a large plot-related cliffhanger during or after the credits (FFVII: the world ends, or maybe it doesn't; FFVIII: Squall dies, or maybe he doesn't; FFX: the plot resolves itself purely due to the nature of its construction [careful planning on the scenario writers' part, in this case]; FFVI and FFIX: each character's future is given a short overview during/after credits). In PoP:SoT, the ending is built such that you know it was meant to be this way from the beginning, although the last boss you just fought seems like it was an afterthought. In this case, was the story or the gameplay climax the most important in the minds of the developers?
Either way, attention must obviously be paid to the genre in question. When we talk about endings in RPGs we're talking about something entirely different than the ending in a Mario game or sports title (should it have an ending at all) where the playing of the game itself is more important than the climax attained from reaching the apex of the game's linearity.
Is replayability an issue? Maybe then the quality of the whole experience must be considered of a higher priority than the immediate aftertaste caused by the ending.