USB 3.0 is electrically and mechanically different. While it is backwards compatible, motherboard manufacturers have to design for users that don't have USB 3.0 jacks on the case as well as those that do, so almost all motherboards today still have both 2.0 and 3.0 connectors to support a wide variety of old and new cases.
Users who want to maximize the number of available USB ports will choose a case that supports both, and they accept that some with be 2.0 and some 3.0.
While adaptors do exist that allow a 2.0 jack to be used on a 3.0 motherboard connector, this represents an additional expense, and the majority of customers are happy populating only the USB 3.0 ports from their motherboard, ignoring the 2.0 ports altogether.
So these cases that support both are intended for those users who want the maximum number of motherboard supported USB connectors, while still accepting that the majority of motherboards have a mix of types.
In another several years you will likely see fewer USB 2.0 ports on motherboards, just a few for backwards compatibility (driver issues with bootable media, mostly), and everything else will be USB 3.0. Cases will follow suit. Until then, you're going to see this somewhat odd mixture.