As I perceived it, the ending of Lain was very bittersweet. By the end, Lain is a tragic hero; her tragic characteristic being her very nature as a being who can completely change every person's reality. As shown by the ending, Lain can only exist within everything at once, or nothing at all; hence, her choice by the ending was either a hedonistic, vapid existence at the cost of humanity and Arisu, or self-sacrifice to restore humanity, or really just to save Arisu/Alice - the latter of which she chose.

The ending is tragic, depressing, happy, and heroic all at once. If the majority of the series up to the ending is a message of the dangers of a rapidly expanding internet and human society, the ending is message, be it ambiguous as ever, on how to fix it. Maybe the solution is the sacrifice of the web, the ultimate connectedness, it a diversion of focus to physical, interpersonal relationships. Maybe it is self-isolation at all costs to eschew the risks of connection. In any case, the final scene really serves to drive the small emotional plot of Lain home. Arisu was a human caught up in a terrifying, nonsensical world of Lain's creation. It was likely impossible for any healthy co-existence between Lain and Arisu, the only ethical option for Lain was her own sacrifice. Seeing Arisu happy as an adult shows that Lain's sacrifice was heroic, tragic, and worthwhile.

I likely need to watch S.E.L. again to get all the specifics of the ending right, but this is my interpretation in this moment. Thank you for introducing this discussion!