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Lets say, for example, one is playing the original mega man for NES on the Wii virtual console. In some situations, there is still a framerate slowdown. I would have thought with the updated hardware that the game would perform better but this is not the case. Why is that?
Because of emulation. To make the game work correctly, it must emulate or simulate the actual hardware it was made to run on.
And to make the game run faster, the hardware needs to be faster, and if the hardware was faster, then everything would be faster.
The thing is that the game isn't compiled for the Wii (or the target platform), but is actually compiled for its original console, and thus needs to be emulated.