Those are some pretty good ones. I do believe Jon is the son of Rhaegar and Lyanna, as there seem to be too many hints in this direction. I also believe Sandor may be alive on the Quiet Isle, but it's hard to know why GRRM would have wanted that.
Jojen does make it to the cave alive in the books. Not sure why they wanted to kill him off in the show, although I think I read that the writers felt they needed to sacrifice someone in that scene given how many undead were running around hacking away at people. Jojen's purpose was to make sure Bran made it to the Three-Eyed Crow, so his job was considered complete.