Well R;N Elite fixes story construction and had parts rewritten since people found the original version of the story unsatisfying and Elite is much better in that regard.
Also Chaos;Head is mostly getting into the mind of a delusional paranoid otaku who locks themselves away. It pulls off an oppressive atmosphere really well it's not S;G levels of good but I think it's worth checking out and you might catch a few things they referenced in S;G.
Delusional paranoid otaku? As in 'seriously', not Okarin's goofy-and-somehow-endearing-on-occasion paranoia?
Chaos;Head Dual (which includes the sequel, I think) is on sale for about Y5300 compared to the regular Y6300 price. Might just go for that and play these games in something resembling their release order. S;G was so amazing. If these others even come close, I'll be very happy. I'm still grooving on the OST and arranged album every day.
(Edit: Just pulled the trigger on the Chaos;Head dual pack. Close to $50, but for two games it should be worth it. Looking forward!)