They really should have never brought Dr.Manhatten into the show at all, maybe have him make a brief cameo and make cryptic statements about what's coming without revealing the details and then he leaves as he considers it all beneath him. Having a group of rednecks (albiet backed by higher up politicians) being able to capture the Dr, is just no bueno.
IMO the show was at its best when Silk Spectre and Sister Night were working as detectives and slowly piecing together parts of the story. Then the last half of the show boils down into a retcon of Hooded Justices backstory to shoe horn in a reason for the grandfather to be at all involved with the story (again, if they stayed away from Dr.Manhatten, this character wouldn't have been needed at all). Then the show spends 2 to 3 episodes working in a love angle for Dr.M that feels very forced. Also the last half of the show removes all agency of Silk Spectre and Sister Night and they either wind up constantly kidnapped or just stare and gawk while exposition is vomitted at them.
Trieu would've been a great villain without working in the Dr.Manhatten angle. Keep in mind outside of Dr.Manhatten, the Watchmen managed to have Ozymandias teleport a giant squid monster into NY and kill a ton of people with a psychic mind blast. With that kind of established material, Trieu could still be capable of doing something really off the beaten path without the need of Dr.M.
The racial themes while not the biggest deal for me in most cases of entertainment, was really heavy handed in this show. To the point where it definitely detracted from the overall quality of the show. The show had some solid moments but Dr.Manhatten and the overly played up racial themes were some big speed bumps in the shows flow.
Oddly enough another show somewhat like this (American Gods) just fired the director/writer of Season 2 because it went incredibly hammy with the same racial themes (there was literally a god/visage of black rage in season 2). They also fired Orlando Jones whose character on the show would play up tensions of black people. In season 1 he seemed to be more of an opportunist/trickster (he's also represented as a spider, so you know the whole tangled webs we weave theme) who knew how to rile up people to suit his own ends, but season 2 made him almost exclusively about racial politics.