Nana Jr. isn't the daughter of the first movie's Nana
Because this is just too sad. It's the same old Nana. However, this Nana's own mother was called Nana too, a fact which a young Jane came to learn (perhaps from a picture book), which prompted us to decide that "to avoid confusion, Nana should from now on be known as Nana Jr." (in her adult-mimicking manner). If you really need an explanation of why Nana would still be alive by then. . . the pixie dust spilled on her in the first movie might have had something to do with it. Hook tricked the Crocodile into leaving
If Hook was able to kill it, he would have long before the movie, seeing as the Crocodile's sole interest is eating Captain Hook, if Hook made the Crocodile think he was dead (by a manner that rendered his corpse inedible) and laid low a while, it's likely the Croc would give up on trying to eat his carcass and proceed to leave the island. Most likely to find something else as delicious as 'the codfish.' The octopus probably came in as a result of the Crocodile leaving, filling the spot it previously had in the ecosystem as 'alpha predator.' The crocodile was eaten by the octopus
This is what I always thought as a kid, and it would probably explain why the octopus also goes "tick-tock" like the crocodile.- Jossed, if you count Jake and the Neverland Pirates as canon. In that show the octopus and the crocodile are seen together at least once.
John and Michael’s reason for being absent is that they are fighting in the war
Considering John isn’t much younger than Wendy he likely joined up voluntarily, wanting to help protect his country. He like Wendy has a wife (or husband) and kids at home who he misses. Michael being the baby of the family isn’t married yet so he was likely drafted being a single man. Wendy doesn’t mention them because she has enough on her mind with her husband being gone and her oldest daughter growing up to fast.- It's even possible that, given the movie takes place in World War II, Michael died in the previous war, like in Peter Pan in Scarlet. This is probably part of the reason as to why Wendy is so close to Danny, because he reminds her of her late little brother (and given the time interval between the two films, she probably had him shortly before she hit menopause).
Thanks to her prolonged exposure to Never Land's magic, between what we see in the first film and in Jake and the Neverland Pirates, Wendy's physical aging has slowed down considerably.
How else (aside from Writers Cannot Do Math) would she, apparently, make it to her fifties without a wrinkle or grey hair in sight? By that same token, Jane will also grow up to look younger than she actually is.