Not sure I follow...
Well yeah, the covanent human war ended, and it is the start of a whole new Chapter in Master Chief's life (a whole new story arc) so naturally it should be different?
And forerunners were already a part of Halo lore, they just weren't the main focus of it.
....Anyways, I still don't see how the new story was any harder to follow than HaloCE...
I mean sure if your new to Halo you won't understand a lot of things, but if you have played the previous games you will easily get the gist of things.....I think it was a story teller from Bungie(interview) that was talking about how you don't want to just spell everything out to the player, but rather get them interested enough to find out more...leave just as many questions as answers.