I'm betting Jiraiya is as dead as a doornail... but it will take a lot of chapters for him to fight his final battle.

Like many other people, I still think Itachi's stated reason for killing his clan was a load of crap. His real reason had to do with whatever was in the temple that he told Sasuke to look for (the Uchiha Shrine). Hopefully, Sasuke and Itachi will just meet to talk instead of fight because it's way too early for an Itachi-Sasuke showdown. Instead, I believe Kishimoto will reveal everything about the Uchiha clan.

I can sympathize with Masa, there are way too many open plot threads right now. Roots seems like an afterthought on Kishi's part - what were they doing when Konoha had no hokage and they're low on ninja's??? They could have staged a coup and taken over easily. I have no idea where the Kabuto/Oro plot could be going, but how about this: he teams up with Root to take over Konoha and install a new hokage. Tsunade and Kakashi die in the battle, and Naruto becomes the leader of Konoha-in-exile. But that's pretty far out there...

Anyway, Kishi needs to do a little clean-up IMO.