Yeah, he was not that great of a guy. Among other things, he was a consistent denier of Japanese war crimes during World War II. Still don't ever condone assassination, though.
The Japanese political system is far less democratic than people tend to assume.
It's essentially a one-party system with managed opposition, and most of the political elite have ties to the far right.
Abe and most of his cabinet, for example, were members of Nippon Kaigi, a far-right ultranationalist organization which holds that Japanese identity is intrinsically tied to the Imperial family, that Japanese war crimes in world war 2 were made up or exaggerated and that Japan should restore its status as a military power, as well as all kinds of pretty unpleasant social views.
Fortunately, the Japanese population is actually quite good at holding the political establishment in check, which is why you don't get the same kinds of problems you do in other managed democracies.
But yeah, there's a reason why interest in and engagement with politics is so low in Japan.