343 Industries has acknowledged that they bungled the story with Halo 5: Guardians. They burnt the cake. They fried the pizza for too long. They cut the custard too deep. I think you get the picture. Well, they plan on fixing the story for the next outing and putting the focus back on Master Chief.
Bungie also tried a similar approach with Halo 2 and also received major backlash for making Chief play second-fiddle to the Arbiter, who had the more compelling story arc in the game. It's amazing 343 didn't learn from that in how they shaped the story in Halo 5.
But what's more is that it wasn't just that it was a lack of Master Chief in Halo 5, it was that for the little opportunities afforded players to step back into his boots you didn't get to play him or Blue Team for very long. The missions that they were in were highly underwhelming and were basically second fiddle to Osiris Team, who seemed to travel the galaxy and take on far more interesting enemies and encounters. Worse yet, Chief didn't even get to meet back up with the Arbiter, Locke and Osiris Team did.
There was just a lot of narrative face-slapping going on where it felt like 343 just didn't have much of a handle on Halo and how to unfold the story in a way that didn't see it unraveling into the disjointed mess that was Halo 5: Guardians.
Even more than that, there was a huge issue with the marketing of the game compared to what the actual game was. The story of Chief and Blue Team going AWOL wasn't really much of the focus, so much as it was Osiris just trailing behind and Locke being mildly aggressive. They missed a huge opportunity to turn Locke into a compelling anti-villain for ONI. While they gave us less of Chief and more of Locke, they didn't do much with Locke at all. I think most fans were expecting more head-butting going on between Locke and Buck over Locke's attempts to capture or kill Chief, and it didn't really happen.
A ton of people were also expecting far more from the physical encounters between Blue Team and Osiris based on how the rivalry was marketed in the ads and trailers. In the actual game, we had one measly little fight between Chief and Locke, and it was highly underwhelming, especially compared to other cinematic fights in games, like the unforgettable encounter between Raiden and Vamp in Metal Gear Solid 4: Guns of the Patriots, or Leon and Krauser's series of intense face-offs in Resident Evil 4.
A lot of people still regard the original Halo: Combat Evolved and Halo: Reach as the two games that have the best story narratives in how they unfold in connection with the gameplay. Hopefully 343 studies both games to get a sense of what made them so great and perhaps they'll get back on track to carrying on the legacy of Halo for Bungie.