Or it can add to the mystery.
If the the NEW empire decimates the Mandaloreans in EP3, the emporer can take over the clones and tech for stormtroopers. In a sense, disbanding the Mandalorean military and outlawing any ties to it (uniforms, etc).
Therefore, in ESB, you have this bounty hunter dressed in a forbidden uniform, yet being called on by the empire to capture our heroes.
That's kind of intriguing...no?