okay, here is a more in-depth explanation as my attempt to put you all out of your misery.
1) the out-of-place things in the wr:
baelfire still being there: as someone said earlier, the wish realm was created by the evil queen's wish that emma had never been the savior. this might not be just because regina failed to cast the curse. it could be for multiple reasons, one being that bae never actually went through the portal and therefore rumple would have never needed to have a curse cast to get back to him. it's possible that bae ran away instead, and rumple killed milah because of that, because she abandoned bae and he blamed her for him running away. in this case, cora could have asked rumple to teach regina magic and she could have found the dark curse herself. also, as for the fact he would have been hundreds of years old by then, obviously rumple would have kept him young using his magic, as we all know how desperate he was not to lose him.
marian being dead: this would have made sense if the above was true, because robin may not have been able to steal the wand from rumple, therefore marian would have died pregnant with roland and robin may have been grieving so much that he changed his name back to robin of locksley and started stealing for himself again in order to help him to forget her.
robin still being young: as was said before, robin was a theif, he could easily have stolen an aging potion or magical object to keep him young.
other various people seemingly not aging: everyone knows magic can keep someone young, it's not unlikely that multiple people did this.
2) biology:
even if hook's grandparents had had two daughters instead of one, brennan and said other daughter may not have had the same child as brennan and alice would have, because even identical twins are not exactly the same. this means that hook's parents must have been the same. hook's parents do not have anything to do with why emma became the savior, except the fact that they had a child who stole rumple's wife. it makes no sense at all why hook's parents would have been different in the wish realm - it's completely irrelevant to the point of the wish realm. hook's parents had to have been the same. and even if alice was wanted or something and went by a different name (which would make no sense at all, where the hell did you get that idea from) it doesn't matter, it's still the same person.
3) hook's life:
whook confirmed that his and original hook's lives had been the same up until the dark curse failed, which makes complete sense. rumple still would have killed milah if my theory was true, hook still would have gone to neverland, it's possible that baelfire went to neverland too when he run away, he could have been taken by the shadow, as it's been proven the shadow visits the enchanted forest, not only our world. if he was taken by the shadow, he still would have met hook on the ship and hook still would have gone back to the enchanted forest to kill rumple.
there's plenty of evidence suggesting that hook and whook's parents would have been the same, and literally none proving that they wouldn't have. i don't understand why this is even a discussion. they're obviously the same.
for those of you who still want proof, i'm gonna try and reach out to the writers on twitter and ask. if they reply i'll be back.