I was initially put off by the character graphics and combat system, but yes it is a good story game. Other people have explained the good parts, so here are some of my personal complaints:

There are some really dragged out cinematics. It seems like they tried to fit some of them to the music, but didn't have anything more to animate, so sometimes it's really long lingering or circling shots.
After certain quests, you end up "having" to spend a long time checking in on companions. And depending on your order of quests, this can happen several times in a row. So it can take out of the quest-flow a little.
There's basically no map. There is an "overworld" map that is very crude and basically just shows "land, sea and major points of interest". Theres nothing when you're in a point of interest. So some areas can be frustrating to navigate, even when they're not supposed to be.
There are parts where characters seemingly make odd or rushed decisions and act as if you should know why already. Almost as if some parts were cut and they forgot to compensate in all related sections.

Personally I'm still not a big fan of the combat, and play mostly for the story. So I'm on story-mode difficulty with mods that increase resource drops and dodge window(it does not deactivate achievements).