I love the first Matrix film, but yeah, the motivation of the machines made no sense. People aren't the most efficient batteries, and you still have to feed them. That food also needs to come from somewhere, and that food needs energy. The sun has been blocked out so it's not going to be solar. Perhaps geo-thermal energy could be used to grow food for the people, but then why not just harness that energy directly rather than losing most of it through a convoluted infrastructure?
The original idea of the machines using humans for processing power made a lot more sense, but unfortunately got kaiboshed by the studio because they thought that people in 1999 wouldn't be able to wrap their minds around such a concept.
In my own head cannon the "real world" in The Matrix is also a simulation. In a world where automation has left humanity without a sense of purpose the ever benevolent machines have created a virtual reality in which people can live meaningful lives. The red pill is a fail-safe for those who do not accept the late 20th century simulation they are initially presented with. It also makes the player feel like they are literally the most important person in the world while encouraging their spiritual growth. This is all my way of saying that the implausible ecology in The Matrix isn't because the film is poorly written, but because Neo is literally trapped in a dumb video game designed to make him feel way cooler than he really is.
As for "great" movies that I don't like:
Inception: I thought it was dramatically flat. The visuals were kind of cool, but not nearly as illogical as a dream world should be, in my opinion. And while a lot of people had their minds blown by this film I grew up watching Star Trek TNG, so I had seen much more mind bending naratives.
Moonlight: The story of a young African American man trying to come to terms with his homosexuality in a rough neighborhood. It could have been good. It even had some strong performances and beutiful cinematography, but it was soooo boring! So little actually happened in this movie, it felt like a 30 minute short that had been padded to be two hours long. The worst part is that the protagonist rarely spoke, or emoted, or did anything at all. A passive and inscrutable lead does not make for a compelling watch.