On the other side Bungie also have IMO the best narative execution in the series with Halo 3: ODST, which I think was a bit of an experiment for them.
I think CE wins for best narrative execution, although its story is deliberately pretty bare bones.
And as for botched narrative, I think 3 ultimately takes the cake when you balance what they were trying to do with what they did. Halo 2 I think of as generally just a bit too ambitious for its own good, whereas 3 had to wrap a bunch up but fumbled badly in the storytelling, especially regarding cinematics.