The "I wish your choices lead to happiness". Is that from author or what Sora says to Aki? It's been bothering me for these past years. If it is the former, then that's cool but if it's the later, Isn't that sounds like they are not gonna be together? It bother me so much I can't sleep soundly every nights :')
Kinda of a late reply but whatever, it's definitely from the author. When I first read it years ago I also needed to figure the meaning of that message, so what I did was look for a raw copy of the last volume, and guess what, that message isn't a translation, it's written in english in the original, so yeah. The only question is if the author is addressing the characters, the readers, or both.
Weather Aki and Sora end up together, well it's pretty clearly left ambiguous but I tend to believe it's hinted they do end up together, I mean the chapter is called Aki's Sora, that is Aki no Sora, that is Autumn Sky. See, through the chapter it seems everyone is getting together or finding their place, but there is an impression that something is off, and then Runa ( I think it's Runa?) spells it out, that something feels off with the season itself, which is Autumn of course. And then in their final interactions, it looks like the wind is leading them to each other, I read somewhere that that's supposed to mean something but I'm not sure. But mostly I think
Clone_Nero got it just right in his analysis of this being Sora real answer to Aki's leaving to him to ask her to stay in the previous chapter, and it's specially true now that Sora knows the whole truth about their parents, that is that their real mother died years ago, now he has all the information to make a informed decision about their future.
Also, and that just may be my impression but I think the latest printing of this manga is a hint on itself. In the original printing in volume 6 cover Aki and Sora are are facing away from each other but in the latest, Aki is wearing in a wedding dress and smiling at us, she never wears this on the manga. It may not mean nothing, but I chose to think of it as a hint of a happy ever after ending.