First, I don't feel that it meets my needs as a Magic design project for the time being. Between the number of reprints and the simplicity of most of the cards, the project is much more about designing an environment than designing cool cards. Without the resources or interest in heavy playtesting, this is not a particularly effective route to practice. I'd rather just work on my cube if I want to practice balancing a format.
Additionally, while I wanted to do the work largely on my own, the complete lack of feedback or attention has contributed to my lack of enthusiasm. Writing this stuff is a lot less fun when it doesn't feel like anyone is reading it.
Finally, the Great Designer Search 2 has been announced. I'm going to be putting a lot of work into card design, and it's going to need to be newer and bolder than M99. This is the smallest of the reasons, but was the final impetuous for me shutting the project down entirely.
That said, I certainly don't consider the M99 project to be a failure. My goal with these things is always to learn, and I've certainly learned a few things about both design and managing myself.
Now, off to go practice...