I think it's safe to say that Naruto is undergoing some rewrites (similar to American comics) recently.
The first thing that happened was they changed the Mangekyou Sharingan around. First it was just three comma's, now it's a pinwheel and in order to get it you must kill your best friend (lame).
The next thing that they undid was Orochimaru's departure from Hidden Leaf Village. Although this can be easily remedied I will say it anyway:
In the flashback scene in the chapter right before the Gaiden Arc, Jiraiya tells Naruto about how he and Orochimaru were in the same position as him and Sasuke when Orochimaru left the village. Jiraiya said he tried to get him to come back, but he didn't. I was under the impression that Orochimaru left after they discovered his experiments. Why would Jiraiya want him back after that? It doesn't make sense, hence this has been rewritten. It wouldn't make sense for Oro to come back and then do those experiments, since I believe Jiraiya said he didn't come back.
Why would they do these things? What is their to gain from it? I believe it has to do with the Gaiden storyline as they will be revealing some major things in it (Kakashi's eye, Yondaime's name, perhaps even Naruto's lineage.) They might not have been able to do some of those things as easily with the old timeline.
I just wanted to see if anyone else noticed this and what they thought.