I have to say that 90s square games generally did this right. I mean, we make fun of it now, but remember Final Fantasy 7, how one of Sephiroth's final attacks was to make the sun go supernova, obliterating mercury and venus, and the expanding star just BARELY touching earth right where your party was standing?
Yeah, it did get old after about the 10th time it happened, but back in 1997 that was some mindblowing shit there.
"Bells, frogs, bing cherries, jingle bells, magic cheese, SEPHIROTH"
I'm with you there all the way. Final Fantasies IV, V, VI, VII, Tactics--getting to the final boss of each of those felt huge. Chrono Trigger did this perfectly. Hell, even friggin' Super Mario RPG built up Smithy enough that going back to Bowser's Keep felt like all had to be put right in the world. Not sure how many people finished Xenogears, but despite the abridged nature of disc 2, the final boss sequence(s) = epic. Also, Earthbound.
But then... oh then we get to other things.
Final Fantasy 8
I did not give a shit about fighting Ultimecia. While the actual scenes, dungeon, and boss forms were great, the game was such a disjointed mess that I didn't care. And it's not because we never saw her--Zemus had that issue in FFIV and it was an awesome fight. But in this one ... eh. There was more going on when you go fight Adel in my opinion.
Final Fantasy 9
WHAT THE FUCK. WHO THE FUCK. WHY THE FUCK. Garland's presence almost neutered Kuja, the final dungeon--awesome as it is--has nothing to do with anything else in the game, the stakes are changed around completely a la Mass Effect 3, and to top it off, the main antagonist is replaced by some doomsday weirdo from the nothingness. And again, Zemus was sort of the same, but it actually worked there. I can see why Square would try the same thing, but they didn't make it work in these later ventures.
And the worst offender by Square of the games I actually gave a shit about from that time period...
Chrono Cross
Considering how artfully Lavos is built up in Chrono Trigger, not just as the antagonist, but as an indomitable force of nature and the catalyst for not only all the game's events, but most important moments in the time and history of that world, the way the villains were handled in Chrono Cross was especially pathetic. Bad guy is Lynx... no wait, you're Lynx. No, Lynx is your father. No, Lynx is a computer from the future of an alternate timeline brought into existence by the defeat of Lavos. No, wait, the bad guy is the dragons you've been helping (one of whom is a French jester somehow) who are actually the divided pieces of a Dragon God from a future where there was no Lavos. No, wait, it's a fragment of Lavos that's merged with a cherished character from the previous game and exists in the darkness of time, none of which has been mentioned before and you only find out about on a beach in the last five minutes of the game from the ghosts of characters from the previous game.
When the party left Terra Tower in my first playthrough, I had no idea what we were doing. It seemed like everything had been taken care of, even if nothing had any relevance to anything else.
What a fucking mess.