Yeah, I'm not entirely happy with 343i's handling of the storytelling in Halo 4, either, on several fronts. The decision to 'kill off' Cortana is one that troubles me, but at the same time it isn't entirely unexpected, given that human-built AI have a lifespan of seven years. What troubles me most about this decision is that Cortana is every bit as iconic to the Halo franchise as the Master Chief, so it'll be interesting to see how 343i handles the storytelling from here without one of its lynchpin characters. That said, I also wouldn't be surprised if they find a way to resurrect her, either through some clever manipulations of the Librarian's echoed self in Requiem (unlikely now that Requiem's a mass of molten metal in a sun that didn't previously exist) or by giving the Chief another copy of Cortana (which would, admittedly, be a less satisfying solution).
I dunno. I'm willing to give 343i the benefit of the doubt at this point, but I'm definitely curious to see where they go with the franchise from here. I'm not certain we've seen the last of the Didact, either (his end seemed a little too... deus ex machina... too easy). Halo 5 should be interesting to see from a story development standpoint.