Sweet! Another fan of Tidus makes me a fan of you. :3
But yeah, the fact that this novel seems to ignore key points established by canon is really pretty weird to me. I have heard that other game-related novels in Japan play along this formula; ignoring parts of canon and having a darker and more violent tone to it than usual, usually because it's the writer's true vision of the game without any supervision from a company or Quality Assurance. This isn't the first time that Nojima displayed his disturbing visions on the game: originally, Tidus was going to be the unsent of the party, but it was given to Auron due to Sixth Sense having a similar plot point. The fact that Tidus is a zombie-like being at the end of the novel and in the drama could stem from Nojima's desire to have him be an unsent.
However, it's not like Square hasn't stripped a novel of its stance as canon before. I remember people talking about how VII's novel (On The Way To A Smile) completely screwed up the storyline of Nibelheim, and they had Crisis Core completely rewrite it to revoke the complaints. I've also heard rumours that Square dismissed the creation of an X-3 due to the worldwide backlash that Will and Eternal Cost got, only saying that it was to 'expand the universe' rather than make a sequel. On that note, it could be possible for them to start an X-3 from scratch and ignore the two added bonuses, especially seeing as how Eternal Cost was only released in Japan, and it's unlikely that we'll get an international release. Will could be seen as a 'what if' story. Or a dream. I dunno.
On another note, I was browsing a thread on Mognetcentral yesterday, and I found some other questionable details from the guy who first suggested the 'boat sex' theory. First up is the fact that during blitzball practice, Tidus has gotten worse at blitzball and can't catch up with the Aurochs. I don't know if it's just rust, though. Either way, it makes him really sad.
Second is at this point, Yuna is still talking to the vilage elders. Tidus then figures that if he made the elders 'disappear,' everything will return to normal and he'll have Yuna to himself... Yeah. Granted, I don't competely blame him, but picturing this depressed Tidus planning a serial murder just... it's disturbing.
Lastly, Tidus spirals further into this depression and starts wondering if Yuna even missed him at all, and begins to hate himself over it.
I can't really say that this is all true seeing as how the 'boat sex' thing was all wrong, but... that predicted what was going to come for us. Reading all the details we have so far makes me wonder if Nojima has a major grudge against Tidus or something. Seriously, this isn't normal. Loneliness, depression, out-of-place behaviour, decapitation and mental alteration, as well as physical hindrance and heartbreak in Will... I mean, damn. There better be a good reason for all of this, like setting up a revenge or redemption story. Some people might find Tidus' suffering brilliant to them, but hell no! This is creepy as f***, and don't you deny it!
Makes me wonder if Spoony struck a deal with Nojima to let him write Tidus' fate, seeing how much he resents the poor guy.