I would basically invalidate the whole fred linda kelly and halsey dissapearing to onyx thing. Or at least move it to after the events on the ark.
Basically, I think Halo 2 (or at least 3) would've been much more awesome if Linda Kelley Fred and Halsey were involved. Glasslands has told us that they are on earth again by the time the tribute cutscene in H3 happens anyways so...they'd all still end up in the same spot.
I just felt that things didn't come together for the characters in the universe for Halo 3. Instead of everyones paths crossing, they got further apart.
Since there are 3 months between the destruction of the ark and the tribute cutscene in H3, then there's the perfect window for all the events at onyx to still happen, a few minor details would have to be changed but H3 would have been much more climactic, IMO.
[Edited on 10.30.2011 11:44 PM PDT]