They've taken a few abilities out, like mute, as well as some game modes.
The only really different thing is that they added a ranking system, called the Abstergo Ladder, as well as clans. I'm not particularly happy about these changes tbqh.
There are a few other changes, but they're pretty minor. Like no compass in AA until you actually steal the artifact. Things like that. --- I found that highly offensive Official Aveline de Grandpre of the ACIII boards