The third reason you give for disliking Gyo is actually the reason I love it. Far too few works of fiction from Japan deal with the subject of that country's horrific actions during World War II. At best, if they discuss the war at all, they depict Japan as an innocent victim of American firebombing and nuclear attacks. But Gyo is different. The Imperial Japanese military's hideous experiments are a major plot device, and it is even implied that the "death stench" gas is being controlled by the ghosts of people killed by the Japanese during World War II. Ito's message is clear-- Japan must acknowledge its past, or be doomed to repeat it.
And in a country as conservative and resistant to social change as Japan, that's a very brave thing to say. I can't help but congratulate Ito for that.