Squaresoft by a mile...Vagrant Story, Parasite Eve I and II, FF7,8,9,10, Xenogears, Chrono Cross, SOTET...many of my favorite games were made by these guys including my all-time favorite: Parasite Eve II.
Yup. That pretty much says it all. Also, PE2 is one of my all time favorites, too.
But then again, even if it was a spectacular failure, FF XIII just tried too hard for me to hate it. I mean, it's one thing to hate a quick cash-in job. It's quite another to try something difficult--like updating classic ATB combat--and fail miserably. Even if most people will never like it for what it is, it just shows too much passion for the craft for me to ever hate it.
It's hard to put my finger on it, but I think something about Squaresoft's corporate culture soured after the merger. I've said before that I think Dissidia Duodecim got Lightning's personality and character better than the original FF XIII did, and that's almost certainly because Duodecim didn't have as much executive oversight. It was a cheap fanservice game which didn't warrant the scrutiny an executive will put on a multi-million dollar project. Chances are, that's choking the life out of the bigger AAA projects.