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There's one other factor to her unexpected death: fear. Major characters were usually not killed off in such games, but when FFVII crossed that line people were shocked and afraid that her death might not be the last (and turn into the video game equivalent of Blake's 7)..
Her one-dimensional character argument on the other hand misses one key point: Players didn't know that Aeris would remain that limited in her character. They were expecting her to bloom later in the game as the heroes approached the story climax, learn more about her which would then develop her character in new ways. But all that was cut short by her sudden and unexpected death. So the players did not just lose the character she was but also the character(s) she might have become. And so they mourned all that lost potential.