My tl;dr is that FFVIII was probably written with an actual plot in mind, but the writers failed to produce an actual storyline. They basically had a sequence of events leading to a particular (and probably clever) twist in mind and didn't do enough to connect them or flesh them out beyond serving as buildup/payout for their twist.
I know I've said this before (like in every thread where FFVIII came up) but I really feel like FFVIII changed writing staff at some point. The gaps in the story don't feel like they happened for budgetary reasons -- it's like there's this really big shift in tone shortly after Disc 2 starts and a lot of the rest of the story felt like it was being pieced together from someone else's notes.
I've said it before, FF8 is my favorite FF game (beat it 3 times), but it is the one I complain the most about. Everything that's wrong with the game, I've probably complained about. The plot with more holes than Swiss cheese, iffy design choices for gameplay mechanics, Rinoa (though I don't dislike her as much as I used to), all valid reasons to dislike the game.
I think we all have one or several of these.
... Also I want swiss cheese now.
For legitsies, sometimes I think the only reason I bitch about games I don't like is because I'm actually mad at myself for being unable to like them.