The campaign shall begin at the very start of Naruto (part 1) and shall continue throughout part 2 (including Kakashi Gaiden) all the way until Kyuubi Mode Naruto is achieved, right before the 4th war. Cyberconnect 2 has confirmed that they are waiting to do the war until Naruto is over so that they can do it all in one, proper sequel to Storm 2. The character roster is to be the largest in any Naruto game made to date (i forget how many, I think it was 80+)
Storm generations is merely storm 2.5 with little changes to the combat system (again, they are waiting for the end of Naruto for an actual Storm 3). The changes that have been added are: a separate substitution bar (instead of substituting with chakra), and combo cancelation, among others.
There has been no confirmation of any boss battles, and it is rumored that the campaign will play similar to Storm 1 (fight after fight with cutscenes in between, rather than the RPG style of Storm 2). On the flip side, in replacement of in game cutscenes, the game will feature over 60 min of original anime content.
Online has been improved over Storm 2, as we now have more online modes. The modes we now have are: vs mode (standard 1 v 1), tournament mode (a classic tournament where roughly 6-8 players can compete with each other at a time. It shall be 1v1, with the other players spectating the current fight, leading to the final 1v1 in the tournament). Also there shall be a survival mode, where a player shall fight endless waves of enemy forces.
Hope this helps!