[Alastor]

Their merging was very much due to financial and economic reasons. When Hironobu Sakaguchi left Squaresoft, he took with him lots of $$ and so those two merged. They're basically not getting too involved with each other's trademark games. For instance, the DQ games are still made primarily by the Enix folks, while the FF games are the responsibilities of the Square folks.

I mean, they're probably involved with each other, but they don't have the same Designer, Director, Producer, etc... those core jobs that make up the concept of the game are still seperated between Square and Enix. So in reality, Square-Enix games that spell Final Fantasy is more or less Squaresoft, minus Hironobu Sakaguchi, who himself was very satisfied with FFIX (as am I).

But, to answer your question, I don't think there's too much of a difference. I love Final Fantasy IX and Crystal Chronicles, and I love Final Fantasy XII. Personally though, I think SE is failing because all I see from them are DQ and FF and KH games. I'm pretty sure they could develop a wonderful game that isn't an RPG or something.