Blade Runner's weak box office performance was easy to predict. A lot of people tried to convince themselves and others that Ghost in the Shell underperformed at the box office over a storm in a teacup controversy, or because it wasn't faithful enough to the source material, or because they felt it simply wasn't a good film on its own merits. But that's really overlooking the essential problem.
Audiences do not like cyberpunk.
Not just cyberpunk, either. Any sort of "gritty" futuristic film is really prone to flopping. DREDD is a cult classic, but it tanked at the box office. The Total Recall reboot didn't do well. The RoboCop reboot was successful, but barely. With the latter two, fans of the older film, or film adaptations try to argue they weren't good enough, but that's just denial. Heaps of films do really well. Cyperpunk and urban dystopia films do not.
There have been moderate successes like TRON: Legacy and AI: Artificial Intelligence, but the genre has a fairly consistent problem. The average moviegoer doesn't care about the source material of Blade Runner and GitS respectively. They don't have any attachment to neon soaked streets. For them, two films may as well have been interchangeable "what does it mean to be human, bra?" stories. One just had better marketing and performed slightly better at the box office while costing a lot more to make thus negating the benefit of higher box office.