Set Star Trek: Discovery in the Kelvin Timeline
You'd think this would be obvious. Bad Robot created the Kelvin Timeline, or the Abrams-verse and after a few movies, a spinoff group called Secret Hideout popped up to handle the franchise going forward. They've been in command of things since 2014, but they still have ties to Bad Robot and the Kelvin Timeline. So much so that we all thought that Discovery would be set in that timeline created by Abrams.
It wasn't, it was set in the main timeline, home of William Shatner's James Kirk, not Chris Pine's. A move that would doom the show. Discovery had the look, feel, and pace of a Kelvin film, and not everyone in Star Trek's fandom liked those films. Those who did liked that they were different from what had come before, but existed alongside the core Trek experience. By forcing Discovery into the main timeline of stories, you changed the concept of Star Trek at its core. Becoming darker, edgier, and less in line with the values that Gene Roddenberry had wanted for the franchise.
By having the show be a prequel to Star Trek 2009, you could've done all the things that Discovery did, but without the massive fan backlash that came along with it. The Klingons we saw in Discovery were far more in line with the ones from Into Darkness, making it so much easier to believe that in this universe, that's just how they looked. Instead, they tried something that failed miserably and it angered a lot of fans.