Truly, there's only speculation on this, but I'll offer my analysis of the facts.
The biggest reason for there not being a second season is money, and second is the many hands in the cookie jar. Addressing the first reason, Square owns rights to this, so in order for there to be a second season, Square needs to either go out of business or dump money into the project. At the end of 2009, they weren't doing so well financially, so probably didn't plan on funding another season to begin with. Stopping production on an already established series generally kills the chances for other seasons to follow (partially logistical reasons) unless it was ridiculously successful and can be cashed in on later. The second point is that there were dozens and dozens of animation companies involved in making this. Redrafting proposals to continue work on this and orchestrating that many different branches of people would be a nightmare.
Also, I heard that the manga that this show was based on was still on going and the series had caught up to the point where the producers had diverged from the source material. To my knowledge, there hasn't been a single series that has done this, taken a break in between seasons without announcing a future season, and actually continued*.
* An exception would be Slayers TV, but that was ridiculously successful at the time of its creation and was an easy cash-in later for the extra seasons a decade later.