Here's why Alien: Covenant wasn't filmed in 3D despite Ridley Scott wanting to use the format. Despite directing the acclaimed original movie back in 1979, Ridley Scott wasn't invited to return for the sequel. While he was later approached for Alien 3 - back when William Gibson was penning the script - and a proposed fifth movie to be penned by James Cameron, it wasn't until Prometheus in 2012 that he returned to the universe he helped create. This project started as a prequel to the first film before morphing into more of a spinoff following a team of scientists investigating the origins of life on a remote planet.
Prometheus was eagerly anticipated and proved to be a major hit when it was released, though its reception was quite mixed. The uneven tone and messy screenplay were commonly cited issues, with the story suffering from logical holes and characters seemingly acting in dumb ways to move the plot forwards. Many viewers also missed the classic Alien design by H.R. Giger, so sequel Alien: Covenant tried to be both a traditional Alien sequel blended with the tone of Prometheus. This resulted in an uneven mix that again disappointed fans, with the return of the Xenomorph also being mighty underwhelming with Scott turning the beast into a generic, slobbering CGI monster.
One thing a Ridley Scott movie could never be accused of is being visually flat, with both Alien prequels offering up gorgeous visuals courtesy of his regular cinematographer Dariusz Wolski. Prometheus was particularly pretty and came along in the 3D wave that followed the success of Avatar. The movie was one of the rare blockbusters that made good use of the format too, and the director once pronounced he would never make a non-3D film again. Cut to five years later and Alien: Covenant wasn't in 3D and for a very simple reason.
Despite Scott's love for the 3D format and wanting to use it again for Alien: Covenant, he revealed in a chat with American Cinematographer magazine (via AVPGalaxy) that the higher-ups at the studio had decided the craze was done and didn't want to use it for the sequel. Dariusz Wolski still infused the movie with a rich, gothic look that helped set it apart from the brighter color palette of Prometheus, with the visuals being one of Covenant's plus points.
It's doubtful critical opinion on Alien: Covenant would have improved if it had used 3D, but at least Ridley Scott is one of the few filmmakers to make use of the format. While the director has talked up a return for a third and final Alien prequel following Michael Fassbender's deranged android David, the disappointing box-office returns of the last entry make another chapter unlikely.