Gibstone, I am not too sure about boss battles but the longbow team has mentioned that they wanted to include more 'set-piece' battles in Rome. If you have played Philip of macedon/Gold then you would have gone through the battle to secure Macedon near the beginning of the game. I think they plan to have more of those scattered throughout the game.
The only thing I know about unit upgrades is what was present in Philip of macedon. Essentially as the units gained experience they could become better at logistics or initiative, etc. I don't know whether they will be expanding upon this system much. Although I do know that some units will be able to traverse marshy terrain while others can't.
Finally, I think they mentioned that there will be special units. I know there were in the first game and I believe that, at the very least, some of Caesar's legions will be special units.