It is like the difference between an apartement block and a high rise!
First the mobo has a dimension with holes specifically made for a given type of case.
Secondly, if you want three cdroms and four hard drives down the line, you have to get a case that will be able to take other devices. Some cases can take one hard disk and one cdrom; no room for expansion. They take less space, but you also have less space!
The choice of your case all depends if you plan to keep it for long to be able to add new devices, or it is like a laptop, practical but barely or no further improvement!