Better on a rewatch but still a few issues.
I feel they should have shown the Lake Herman Road attack and cut the Kathleen Jones car incident given the fact LHR is a verified Zodiac attack and the Katleen Jones incident is likely unrelated. I get the LHR attack occured half a year before the Blue Rock Springs attack (which was the opening of this movie) so a time jump would be required but this movie had so many of them anyway... perhaps it could have been shown later in the movie as a flashback sequence once the Zodiac takes credit for it during his first letter sent to the San Fran. Chronicle? They condensed all the Zodiac attacks into the first half hour of a long movie, a bit more breathing room and time between would have been better.
The movie was going well with Gyllenhaal, Ruffalo and Downey Jr. sharing screentime but just past the half way point it becomes the Gyllenhaal show, he's a good actor and done well in the role and I get part of the movies story is how he becomes utterly obsessed with the case but at 2hr42mins the movie could have cut that second half down a bit and not lost too much.
They should have cut out all the Richard Marshall stuff. The scene in the basement is maybe okay on a first watch at tension building and it does show how paranoid Gyllenhaal's character is becoming but it's unnecessary.
Lastly and this will always be a big issue. The heavy focus on Arthur Leigh Allen is grating as someone who doesn't think it was him. They shouldn't have leant so heavily into the Allen is guilty theory.
I like the movie but want to like it even more than I do. I have an interest in the case and this movie has talented personnel doing good work but a few things just let the movie down a little.