Clearance above the board. With my last case, I went through 3 motherboards before I found one that could fit my radiator and fans above the board because the shipping was cheaper on the boards.
The Width of the case. I want a case that will be able to hold a large video card + a huge heat sink for the processor.
Thin cases don't always have room to do that.
The most important thing when deciding upon a case it the engineering & consideration of the design. Good airflow, quiet fans, easy access to internal components, adjustability, etc.