Yeah, Mangekyos could look different depending on the person, be it from the type of Jutsu they prominantly use, or the method of which they evolved their eyes to it. After all, Mangekyo just means Kaleidoscope, and both Kakashi and Itachis follow the same pattern, just with a different look.
Though, Kakashi still suffers for not having an Uchiha body, nor the chakra levels of an Uchiha. Perhaps that could be what causes his to be different from Itachi.
That and Kakashi has Magenkyou in one eye rather than two like Itachi does. Wouldn't that make a difference?