You can't blame one game as the catalyst for turning the Halo story into a convoluted mess. Halo 4 introduces the Didact as the new antagonist, yet his inconsequential actions create a circular story. In Halo 3, the Flood army changes sides more times than the Italians during World War 2. Regardless of what happens, somewhere in the galaxy, Covenant and Prometheans forces await the Master Chief's arrival. They wait for you to shoot them.
Halo 5: Guardians re-threatens the entire galaxy because we need a reason to shoot aliens. Not much motivates a faceless, robot-like character to risk his life to save everyone, again. To push Master Chief aside, 343 Industries brought in new characters - Spartan Locke and the rest of Fireteam Osiris. But even four new major characters can't define urgency in Halo 5's story. It doesn't matter why Master Chief and Spartan Locke shoot the Prometheans and Covenant - it stopped mattering. Halo 5: Guardians adds long overdue adjustments to movement and weapons to renovate what matters most: gunplay. And the evolution of Halo's core gameplay will last longer than any convoluted space opera about saving the galaxy.