I had no problem with the FFXIII battle system. At least it was something different, and I could do with one more. I'll agree with most people that the thing that trashed FFXIII was how random and bizarre the story was. They got so far off the deep end with their weird fantasy elements, that it was impossible to relate to. And since all of the characters' struggles were DIRECTLY related to unfathomable fantasy weirdness, it was difficult to sympathize with them.
I love Fantasy and Sci-Fi... a lot in fact. But it has to be done right. It has to be applicable, and used to explore applicable concepts, at least at some level. If the human relationships are too divorced from our own experiences, than it's very hard to relate to them, and suddenly the emotional core of the story becomes meaningless and impossible to sympathize with. In ANY story (sci-fi or not), if I can extract some basic human framework, removed from the specifics of setting or plot, then the writers have succeeded.
Contrast FFXIII with Nier. If you really dive into the world of Nier's backstory, it's pretty out-there, just as random, illogical, and nonsensical as FFXIIIs. But all that random mumbo-jumbo is pretty irrelevant to the individual character struggles and relationships within the confines of the game. So you can still sympathize with the characters, even though their situation is so incredibly goofy. The basic conflicts are fairly universal, even if the underlying reasoning isn't. That's how Nier works. If Nier had brought up all it's weirdness right upfront, made up dozens of mumbo-jumbo keywords and descriptions, and shoved it down your throat at every given opportunity, it would have been SHIT.
And that's where FFXIII went wrong. The writers reveled in overly-complex, overly random, hard-to-conceive bullshit, and had to bring it up every chance they could get. I don't believe that FFXIIIs back story is any worse or weirder than Nier's, but the fact they had to call your attention to it every 3 seconds was detrimental.