Uh... cause I like the story more than the gameplay? I like the gameplay too obviously.
My major gripe with the gameplay in XII isn't the combat. It's just that a lot of the areas are irritating to traverse. It's not too big a deal most of the time. More of an annoyance really. A few people have already mentioned the end-game areas, and yeah, they're the absolute worst. If only they shortened some of those areas and made the real final area (one of the weakest final areas in the series) a bit longer/better.
Although you know what? I never thought of this until now, but it sure would make a lot of sense to consider the second-to-last dungeon as the real final dungeon and the actual last area as sort of just the final boss' room/lair/whatever. Looking at it in that light actually puts a slightly better taste in my mouth.
Regardless, I can actually kinda forgive those last couple areas anyway cause... well, there are actually events there that advance the plot. For so much of the game it just felt like absolutely nothing was happening. The game always had you going to some or another new location, but most of the time once you got there it felt like not much really compelling happened.
Of course I think you can chalk a lot of that up to the characters, and the characters you can chalk up to the "troubled" (I guess?) development of the game and perhaps the developers' intentions/goals/vision for the game. I think maybe those intentions/visions kinda clash with what I (and no doubt many others) want and/or expect from a Final Fantasy game.