On the topic of Namine, I would be quite curious if she became some other entity, similar to how Xion turned into all those forms at the end. I don't mean Namine has to become a hulking beast, but she is special, so I think it would be cool if, along the story, she either manifested into something else and became a boss or something, IDK. If not I'm completely fine with that too, but she seems to powerful to not be an decent helper or ally in a fight.
As for my wish, I honestly want them to somehow allude to the "Sora! Dinner's ready!" from KH1. They don't have to directly reference it by Sora saying "Oh darn! I never had dinner that night I left the island..." or something cheesy like that, but I've said it before I know, if you ever go back to DI (I see that as highly likely in KH3 for you to be able to finally visit DI again) maybe Sora can go to his house and there will be whatever he had for dinner on the table. You could interact with it and when you did maybe a small textbox would pop up like "A plate of (insert food here). Looks like it was never touched and it is cold now." something like that.