I really love the way that Tidus tries to run afterYuna to help her, to save her from a huge scary fiend, but really she's just running the Gunner's Gauntlet.
Yuna's job as a digger in Bikanel Desert is another wonderful thing to use to show Tidus that Yuna just isn't quite the same as she used to be. I really enjoy the way she defends herself so much, the way she won't back down about what she wants to do with her time.
I think that you definitely chosen the best difference to be the breaking point in their relationship. Given how Tidus feels about blitzball it must kill him to be pushed out and made obsolete in that arena as well.
I really enjoyed this exploration of what might have happened to Yuna and Tidus' relationship due to the changes in Yuna's personality. You make some excellent points about their possible incompatibility. I really enjoy the activities of Yuna's that you choose to emphasize as making her 'different.' I'm not sure that I can actually see Yuna being as cross and annoyed as you made her, but I appreciate that it could happen to anyone no matter how sweet and caring after awhile.
I found this a very interesting read.
"Two years changes thing, haven't you noticed that yet?"" Replace "thing" with "things."
"And I will not releasing Brother from his contract unless he wants to go." Add "be" before "releasing."
"It all started when I saw that sphere I thought was you."" Yuna didn't think that Tidus was the sphere. So maybe change this to "when I saw that person in the sphere, who I thought was you" or something.
""But, if you haven't, I would have stayed in the Farplane forever."" Replace "haven't" with "hadn't."
One other nitpick and this is a bigger one. You really use a lot of italics in this story. It sort of distracts from the story itself after a point. I think that using italics ocassionally for emphasis is a good choice, but using them to excess just makes them lose all meaning.