You're playing the wrong games if you want story.
Ultimas 1-3 were messing around. The series became more serious with the fourth game and Ultimas 4-7 are easily the most thoughtful and best written oldschool (pre 1997) RPGs and they still hold up - they're just so oldschool that they're not a good starting point unless you have balls of steel.
http://www.rpgfan.com/features/Top_20_R ... 90s/3.htmlhttp://www.rpgfan.com/features/Top_10_B ... tten_RPGs/http://www.rpgcodex.net/content.php?id=8869http://www.complex.com/video-games/2011 ... -in-games/ (durr Resident Evil has better story than Xenogears or PS:T, fucking OOT as number one etc, yeah I might not agree with this list but it still confirms those RPG lists are saying, it has BG2, SS2, PS:T and Deus Ex on it)
This is all you need to know, though the inclusion of certain "new school" RPGs and the lack of oldschool RPGs is surprising in the RPG codex article, given that that's the site for angry elitist oldschool RPG gamers
So anyways, Planescape: Torment is the place to start from. Everywhere you go, it's praised as the best written RPG and the best written game of all time. If you like the adventure game Longest Journey (another game that's often praised as one of the best written video game stories), you'll like Planescape: Torment.
After you're done with Torment, you have few different choices where to go next:
1. Isometric games in done in the same style as Planescape
Fallout 1&2+Baldur's Gate 1&2: This is the FF6&Chrono Trigger duo of CRPGs.
If you want an alternative to those, or you're looking for more, there's Arcanum. Another isometric RPG. Not as much praised for it's writing as Fallout and Baldur's gate games, this game's strengths are it's unique steampunk world and the level of depth, choices and freedom in character creation and roleplaying.
Both Fallout 1 and 2 are equally great although different from each other, but Baldur's Gate 2 is a lot better than the first one. So you're getting a more uneven experience with the BG-series.
2. If you can tolerate more action heavy gameplay and first person view, there's the
trio of FPSRPGs
Deus Ex, Vampire: The Masquerade - Bloodlines and System Shock 2.
All of these are quite heavy on combat, VTMB has the most social interaction and dialogue and you can talk your way out of fights. You'll read a lot of emails and listen to conversations and audio logs in Deus Ex and System Shock 2, so even though you're alone fighting most of the time, they still have a very strong narrative (and amazing stories). Deus Ex is often praised as the best game of all time thanks to it's plot (it's very Bioshock-esque, but it actually has more to say than Bioshock or Bioshock Infinite so I'd rate it as a more intelligent story because of that). System Shock 2 might be the least appealing to you out of those 3 games because it's a survival horror game and the plot is very scifi-y, but as a game it works best out of the three. And it has some deeper, symbolic conflicts going on it's story.
3. Anachronox
"Western JRPG"
With the exception of Vampire and Arcanum (more obscure), all of these games are lauded for their excellent writing and stories. That doesn't mean they're poorly written though, especially Vampire has some of the greatest characters and dialogue that I've seen in a RPG. If you can play through a modern Final Fantasy game, you won't have a problem with any of these games if you're looking for a good story, because they're all a lot better than any X-series Final Fantasy.
After you're done with that top 11 list, feel free to try modern or oldschool WRPGs.