LV 99 final boss boost... That is some crazy grinding right there.
I'm not asking for Superbosses to disappear, I'm just saying not every RPG needs one.
You're saying that having a superboss automatically makes a game "weaker", so you kind of are asking/suggesting that they not be included.
As for crazy grinding - getting to level 99 in a FF is nothing. They all have some high level grinding area for you to go to (dinosaur forest in FF VI - getting that great esper from the Brontosaurus or whatever it was). Try playing a stat-maxing game in Xenosaga 1 sometime. Or a complete sphere grid maxing game in FF X (which you pretty much have to do in the PAL version - sadly not available in US to beat Penance).
As to what made the Xenosaga 'superbosses' great? The Erde Kaiser's had their own storyline, both in the main plot and as a side quest. Xenosaga 2 made you continue the game after the game over in order to do the Dark Erde Kaiser fight and a couple of other things. The super Erde Kaiser in Xenosaga III is visible as soon as your character starts the game (after a short combat prologue). You can try to beat him all you want, but you can't win until you collect the three skills to break his shields, then the real fight begins. Xenosaga was also pretty unique in that the guy who is the 'antagonist' for most of the series and the one you're really going up against at the end is the Protector of the Universe - which is why he still helps you at the very, very end: you screwed up his plans, but he's still got his job to do... Xenosaga III also had a 'superboss' in the weapons development center (a good place for one, don't you think?)
Generally speaking, the final boss is for people who play the way you seem to enjoy: no grinding, just going through the game fighting what you have to and collecting what you can. Final Fantasy's have always had a very low bar for the end boss (see: VLL games in FF IV or V, the solo white mage for FF 1, and I know you can beat the end boss of X-2 at level 30 if you have the Dark Knight class and alchemist leveled).
Superbosses are for players who like the grind. who want to squeeze every ounce of potential power out of the game. The ones that level up on weaker opponents if it means their stats will rise more (Xenosaga I), or else doing things like maxing out every esper, or getting the ultimate weapons (Dark Cloud 2), or whatever.
The great thing about including superbosses is you've just expanded your game's potential audience to include both groups of players.