Here is how you fix Season 3.
Timelines
Condense the 3 timelines into 2. Having the three timelines was needlessly complicated. In the 1980's timeline, West & Hayes are about age 35, the 1990's they are about age 45 and in 2015 they are about age 70.
As an alternate timeline to the events, have things kick off again in 1980. Then, skip the whole Woodard, discrimination of a Veteran story-derail. Have this timeline culminate with Tom's "suicide". Jump forward in time to year 2000, where West & Hayes are at the end of their careers and they get a finger print hit on Lucy Purcell, resurrecting the cold case for one last hurrah to their careers. One thing leads to another, they kill Harris James around episode 5, and then bring in Michael Rooker (Hoyt) as the big bad for a true culmination to your story.
AARP Club
A large portion of the season was spent with the elderly Wayne, trying to remember where he was and what he was doing. His missing memories where a plot device to hold back information and drag the season out. The impact at the end of the story was pretty minimal and more frustrating than anything else. It had hints of
Memento, themes of frailty and regret. I'm not sure what this timeline did to serve the overall story.
Just skip this timeline and put your effort into a year 2000 timeline as mentioned above.
Amelia
For someone that played such a pivotal role in the story, there were some very odd things about her character. Hints that she lived an alternate/double life in California that was never fleshed out? The jump from grade school teacher to national best-selling author is kind of a stretch? Wayne being about as shitty as a husband and partner to her as possible, yet she completely accepts him as he is? The way the last episode played out, I guess Pizza clearly wanted to say that this season as as much or more about Wayne and Amelia as it was two missing kids?
It is called True Detective, not True Romance. Amelia is a fine character, but to end this season on this note of them maneuvering through their relationship is questionable.
Harris James
Poor casting choice with Scott Shepherd. This is the character that killed Tom, Dan, and Lucy, but whenever he is on camera he comes off as a nervous little bitch.
-Here is what you needed out of the character: Deceptive, Capable, Flexible Morals, and Dangerous.
-Here is how Scott Shepherd played him: Cowardly, Anxious, Family Man, and an Opportunist.
Some guys just aren't the right person for the role and I would argue that they made a misstep here. Cast someone with some backbone.
Roland West
He was the perfect good guy. Too perfect, for a story and world like this. It took 8 episodes before Pizza gave Dorff's character some character. The bar fight scene may have been his best of the entire season, yet it felt out of place because Pizza wrote him to be such a vanilla character that you cannot fathom him walking into a bar and doing what he did.
The bar fight should have happened around episode 3 and been one of the concluding events of the 80's timeline. He should have then showed signs of volatility throughout the rest of the show. It would have been a good balance to his care-taker nature he displayed with Tom & Wayne and given him some depth.
Conspiracy Reporter
It feels like HBO gave Pizza some notes saying,
"You know, people really liked Season 1. Any chance you could tie this new season and the first together?" This was Pizza's half-assed attempt at appeasement. It also felt like his way of taking a shot at the "Lost- Conspiracy theorists". We get it, writers hate when people take their work and spin up some crazy theories, then get disappointed when the story doesn't play out like they wanted. But, when you are writing a show about mystery and intrigue, people are going to theorize about mystery and intrigue.
Either have a purpose to this story-line and character, or remove her out of the story.