First of all, I don't see how Jiraiya never use sage mode against Orochimaru is even a plothole if you even remember correctly, Jiraiya strength was drained and his health issue due to the sake he drank when Tsunade poisoned him. Furthermore where did it ever state that if he doesn't use the sage mode, it's consider a plothole????? Plus it takes considerable amount of time to gain nature chakra.
The whole thing that you explain about element, can you please clarify more, In't understand your point.
Tobi voice is semiplothole so I guess I can give you that since it never explained how he can do that.
Thats your opinion if you hate with Kakashi, Yamato, and Itachi, I find it plausible to the story, it makes sense and I don't understand how it's even a plothole plus it's a filler...
Only thing that what you said really makes a plot hole is Itachi timeline messed up...