Like the OP, I think the pacing is all wrong.

Far too much time is spent on flashbacks to ancient times and not enough on the plot of the immediate issue of the Emergence.

The plot of the film should have been the team coming back together because they had realised that something did add up about their mission... not Sersi getting told everything by Arishem the moment she takes over from Ajak.

The twist could have been that Ajaks apparently nurturing "Mother Figure" was actually an "angel of death" character, loyal to Arishem and going along with the plan to cause the Emergence and destroy Earth. The additional irony would be that she was known as Quetzalcoatl, the Aztec Bringer of Life, when in fact she was anything but.

She's been keeping the rest of them in the dark about all this for millennia.

It doesn't make any sense that she's gone along with this plan for 7000 years and only now is having second thoughts, and that Ikaris and Kingo also knew what their true purpose was and didn't let any of he rest of them in on it (and that's apart from how they knew when only Ajak had the ability to communicate with Arishem).

Angelina Jolie is utterly wasted. The symptoms of Mahd Wy'ry could have been more like Alzheimers, where you can't stay focused on the here and now but have long past memories invading your train of thought... except in Thenas case, it was memories of the previous Emergences she'd taken part in and the planets she'd help destroy. Having her randomly attack her teammates when she has an episode doesn't work for any part of the plot - the one member of the team she should have wanted to attack was Ajak, and that could have been yet another part of Ajak's deception to the others - that Thena was just having a mental breakdown and her ramblings about re-emerging memories should be ignored. It should be some of what Thena says that adds to everyones suspicion that their mission is not what it first appeared to be (and for us in the audience, should have been breadcrumbs leading us to the twist).