Essentials changed more than that. There was a wave of errata, the skill challenge mechanics were changed (I stuck with the old ones), the Monster Manual was made obsolete and replaced by better ones, the feats in the PHB were generally made obsolete and replaced by better ones (such as the expertise feats), and more.
You could still use a pre-existing character in the new version of the game without having to ask "where's the Use Rope skill gone" and "which version of Haste" are we using and "does Spell Resistance apply to Stinking Cloud?" (or just about any other conjuration spell) the way you did if you tried to mix 3.0 with 3.5.
D&Done looks to me as if it will be more like Essentials than 3.5.