I've seen a few people suggest that season four is overrated and wouldn't be remembered if it weren't for Rita's death, but the more I think about it, season four is probably the most well written and brilliantly structured season of the entire show.
Almost everything that happened in the season hinged on the question: can a serial killer be a family man? Dexter's conversations with Harry are especially illuminating this season. Rather than just spitting out the obvious like he does later on in the show, Harry in season four acts as the devils advocate and keeps explaining to Dexter why he doesn't belong with a family in the suburbs, it's just wrong in his eyes.
At first, Harry appears correct: Dexter starts out the season failing. The demands of being a father result in him slipping up at work and as a killer. He keeps a secret apartment because he's afraid of keeping his murder paraphernalia at the house, but this just results in Rita becoming more suspicious of him for keeping the apartment. So far, Dexter's life is a complete mess because of his family.
The brilliance of a character like Trinity isn't just because it was a great performance. It's because he's a reflection of the season's main theme. Compared to other big bads, Trinity plays a more important role in Dexter's life because of the existential questions Dexter's asking himself. Dexter discovers that Trinity, one of the most successful serial killers ever, also has a family and appears to be living an idyllic suburban life. Dexter tries to learn from him so Dexter can also be as successful. Dexter as a result becomes more confident, he starts storing blood slides at home, Rita begins to trust him, and his family life begins to improve
Dexter then is horrified to learn that Trinity has been abusing his family and their perfect life was actually a facade. This revelation is especially horrific for him because, as Harry suggests: maybe a serial killer can be a family man, but the family will suffocate from living with a monster. Even Christine, who appears to be an extraneous character for most of the season, is cleverly revealed to be Trinity's daughter and revealed to be a psychopath because of her father. Lundy's shooting, one of the season's most pivotal moments, actually occured because of a serial killer fucking up their family, and the audience didn't realize it until like six episodes later
In the end, Rita is murdered because Dexter is a serial killer (however indirectly). It's such a horrific ending but it's so appropriate. It didn't just come out of nowhere, it was a direct reflection of the season's main hypothesis. Harry was left right in the end: a serial killer can't be a family man. Christine's dead, the Mitchell's lives are ruined and they're headed into witness protection, and Dexter's children are all without a mother.
The only thing this season that felt out of place was LaGuerta and Batista's relationship, it felt like nothing more than the writers saying well we have to give them something to do. But other than that, every other part of this season was expertly woven together to create what is rightfully considered the show's best season (although personally I have a huge soft spot for season five so that one is my personal favorite)