I'm sticking with the fact that MGS2 is godaweful, imo.
Anyway, story is divided into two sections, script, and character development.
Usually the deepest storylines are some of the most mediocre. Therefore, I will forgoe a "deepest storyline" list, and just say that Baulder's Gate 2 probably wins that argument.
IMO, and in most JRPG's like Disgaea or GrimGrimoire, character development is by far the leading draw. So, I really love character development, and care very little about the overall script as long as I make friends with my characters, so that said, my list in no particular order goes:
Final Fantasy VIII
Chrono Trigger
Phoenix Wright series
Metal Gear Solid 1 and 3
Fire Emblem: PoR/RD entries
KOTOR
FFX
Tales of Symphonia
FFVI
FFVII
Disgaea
These are some classic games that you can ply only for their storylines and they will be good. I'm sure I'm leaving a few out though.
Vagrant Story, FFTactics, Killer 7, and FFXII fall into that deep storyline with no character development mold.
I don't need your console war.
It feeds the rich while it buries the poor.
You're power hungry, spinnin' stories, and bein' graphics whores.
I don't need your console war.
NO NO, NO NO NO.
