Oh man, I loved Star Ocean: until the end of time. That game had a great story with a great twist. The latest one on the 360 had elements of a good story, like for example how they played off actual scientific theories and such when making parts of their sci fi settings. But there were a lot of flaws, especially in the character development department... Was still a good game though. Probably the 2nd best rpg this gen next to ToV.
As for the FF series... I know this sounds like a cliche fanboy, but FFVII was probably my favorite offline FF game. Everything about it was just amazing for it's time. The characters were some of my favorite of any game to date, (with my favorite being torn between cloud and red XIII) the story was really good, with a very classic feel of the good guy underdogs vs. the big evil machine of shinra. The materia/mako thing as well as the weapons, summons, etc. were all implemented very well into the game and story. And the actual gameplay was almost peerless, especially considering it was all done on the original playstation. And despite the whole post ffvii atmosphere ruining it by over doing it, you have to admit that back in the day, jenova/sephiroth made for one of the better villains out there.
As for FFXI, I also really liked the lore in that game. They did a very good job on it, and it really felt like a robust digital world was layed out for you to explore. FFXIV has a long way to go before it's ready to fill the shoe prints that FFXI has left, but I think it will get there eventually.. They have a solid foundation in place, they just need to build on it, but it will certainly take a lot of time and dev hours to get there, so let's just hope that SE has the follow through, and can manage it without compromising the integrity of what sets the FF mmo reputation apart from all those other hack and slash mmos.
The thing with lore in games, is that if the story is going to hype something up as a super powerful villain, and then when you fight him he's a cinch, it just kind of kills it... For example, I remember in FFXI when some friends and I got to the mission where you found out about that guy from jeuno being evil, and you had to fight him. I've heard how much easier that fight is now, but back then, he was pretty **** fierce... You watched the cinema, got all ready for a fight, and then had to go toe to toe with this evil traitor knight in shining white armor, and he would oneshot the bejebus out of you with his weaponskills if you weren't careful. A tough fight really adds weight to the story... So far in FFXIV, not much of the lore has stuck with me, because you just kind of breeze through it. They talk all big, and then you fight a couple easy prey trash mobs, and it's over... Like wth, they could have sent a couple lone troops to take care of that, why all the fuss...