I just ran a PC emu of Kega Fusion side by side with my Wii's Virtual Console version of Sonic The Hedgehog (Mega Drive, PAL). The emulator was set to 22050khz for sound and for video, any semblance of a filter was disabled, with only the 'normal' setting checked in the options for video. I had a Mega Drive, which was slower than the NTSC Genesis.
In terms of speed:
I managed to get the Virtual Console game and Kega Fusion to reset at the same time. With the both going through the logo and title screen at the same time, the speed I'd say is identical.
In terms of video:
The first thing I noticed is that the Virtual Console version's colours are slightly darker in general, and sonic is more of a darker blue than in the emulator for example, and same for the 'SEGA' logo at the start. I remember Sonic this way..
The second thing I noticed, with the emulator in full screen, is that the 'blockiness / pixels' are not as sharp as the virtual console version, in that they are slightly 'filtered' in comparison. This 'filtering' is what I refer to about other emulators.
In terms of sound:
The sound from the virtual console version in terms of the rings and even the sound of the sign pole at the end sound accurate to me.
The sound from Kega Fusion not only sounds 'too good' in a way, with the addition to Kega Fusion of playing more sounds at the same time than the Mega Drive could (like hearing every ring being collected which would not happen on the Mega Drive), but the sound of the sign post is definitely quite distorted.
Albeit the Wii's output is more crisp in general, with that aside, I feel the Virtual Console version is more accurate to how I remember the original Mega Drive than Kega Fusion or generally any other emulator I have used.
I do not have my original Mega Drive any more though, but it is like I remember..