There was nothing wrong with the storytelling about the MC or Cortana, but the greater story about the Forerunner, the UNSC, and there Covenant splinter factions was severely flawed, and that was the story that the whole 343i series needed to succeed. I mean, once Cortana is dead, they need some other draw for books and games.I wouldn't say it or 4 are bad, exactly. 4 has a few, somewhat serious issues, but nothing that really damages my ability to enjoy it or that undermines the story it's telling about MC and Cortana.
Halo 4 is "aggressively not good" on its lonesome. Once you throw in Spartan Ops and the Kilo 5 Trilogy, it is worse.